3HKZ | pdb_00003hkz

The X-ray crystal structure of RNA polymerase from Archaea

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
V [auth U]	SCOP2B Superfamily	RPB6/omega subunit-like	8078381	3000189	SCOP2B (2022-06-29)
I [auth K]	SCOP2B Superfamily	RPB6/omega subunit-like	8078381	3000189	SCOP2B (2022-06-29)
U [auth T]	SCOP2B Superfamily	RPB5-like RNA polymerase subunit	8063564	3001722	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RPB5-like RNA polymerase subunit	8063564	3001722	SCOP2B (2022-06-29)
T [auth S]	SCOP2B Superfamily	RBP8/CHS5 N-terminal domain-like	8093032	3002702	SCOP2B (2022-06-29)
T [auth S]	SCOP2B Superfamily	RBP8/CHS5 N-terminal domain-like	8093393	3002702	SCOP2B (2022-06-29)
G	SCOP2 Family	RNA polymerase subunit RBP8	8046455	4001942	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	RBP8/CHS5 N-terminal domain-like	8093032	3002702	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	RBP8/CHS5 N-terminal domain-like	8093393	3002702	SCOP2 (2022-06-29)
S [auth R]	SCOP2 Family	RNA polymerase II subunit RBP4 (RpoF)	8107701	4002844	SCOP2 (2022-06-29)
S [auth R]	SCOP2 Superfamily	HRDC-like	8107702	3000132	SCOP2 (2022-06-29)
Z	SCOP2B Superfamily	RNA polymerase subunit 13, Rpo13-like	8093030	3002666	SCOP2B (2022-06-29)
M [auth Y]	SCOP2 Family	RNA polymerase subunit 13, Rpo13-like	8047258	4005531	SCOP2 (2022-06-29)
M [auth Y]	SCOP2 Superfamily	RNA polymerase subunit 13, Rpo13-like	8093030	3002666	SCOP2 (2022-06-29)
X [auth W]	SCOP2B Superfamily	RNA polymerase subunit RPB10	8063364	3001213	SCOP2B (2022-06-29)
K [auth N]	SCOP2B Superfamily	RNA polymerase subunit RPB10	8063364	3001213	SCOP2B (2022-06-29)
W [auth V]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8080732	3001655	SCOP2B (2022-06-29)
J [auth L]	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8080732	3001655	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
V [auth U]	RNA_pol_Rpb6_1	e3hkzU1	A: alpha arrays	X: RPB6/omega subunit-like (From Homology)	H: RPB6/omega subunit-like	T: RPB6	F: RNA_pol_Rpb6_1	ECOD (1.6)
I [auth K]	RNA_pol_Rpb6_1	e3hkzK1	A: alpha arrays	X: RPB6/omega subunit-like (From Homology)	H: RPB6/omega subunit-like	T: RPB6	F: RNA_pol_Rpb6_1	ECOD (1.6)
U [auth T]	RNA_pol_Rpb5_C	e3hkzT1	A: a+b two layers	X: RPB5-like RNA polymerase subunit (From Topology)	H: RPB5-like RNA polymerase subunit (From Topology)	T: RPB5-like RNA polymerase subunit	F: RNA_pol_Rpb5_C	ECOD (1.6)
H	RNA_pol_Rpb5_C	e3hkzH1	A: a+b two layers	X: RPB5-like RNA polymerase subunit (From Topology)	H: RPB5-like RNA polymerase subunit (From Topology)	T: RPB5-like RNA polymerase subunit	F: RNA_pol_Rpb5_C	ECOD (1.6)
T [auth S]	RNA_pol_RpbG	e3hkzS1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: RNA_pol_RpbG	ECOD (1.6)
G	RNA_pol_RpbG	e3hkzG1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: RNA_pol_RpbG	ECOD (1.6)
S [auth R]	RNA_pol_Rpb4	e3hkzR1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: RNA_pol_Rpb4	ECOD (1.6)
F	RNA_pol_Rpb4	e3hkzF1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: RNA_pol_Rpb4	ECOD (1.6)
E	S1_1	e3hkzE1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
E	SHS2_Rpb7-N	e3hkzE2	A: a+b two layers	X: Dodecin subunit-like	H: Flavin-binding protein dodecin-like (From Topology)	T: Flavin-binding protein dodecin-like	F: SHS2_Rpb7-N	ECOD (1.6)
R [auth Q]	S1_1	e3hkzQ1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
R [auth Q]	SHS2_Rpb7-N	e3hkzQ2	A: a+b two layers	X: Dodecin subunit-like	H: Flavin-binding protein dodecin-like (From Topology)	T: Flavin-binding protein dodecin-like	F: SHS2_Rpb7-N	ECOD (1.6)
Q [auth O]	RNA_pol_L	e3hkzO2	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L	ECOD (1.6)
Q [auth O]	RNA_pol_A_bac_1	e3hkzO1	A: a+b complex topology	X: Ribosomal protein TL5/L25 C-terminal domain-like	H: Insert subdomain of RNA polymerase alpha subunit (From Topology)	T: Insert subdomain of RNA polymerase alpha subunit	F: RNA_pol_A_bac_1	ECOD (1.6)
D	RNA_pol_L	e3hkzD1	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L	ECOD (1.6)
D	RNA_pol_A_bac_1	e3hkzD2	A: a+b complex topology	X: Ribosomal protein TL5/L25 C-terminal domain-like	H: Insert subdomain of RNA polymerase alpha subunit (From Topology)	T: Insert subdomain of RNA polymerase alpha subunit	F: RNA_pol_A_bac_1	ECOD (1.6)
P [auth J]	RNA_pol_Rpb2_6_3rd_2	e3hkzJ1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_2	ECOD (1.6)
P [auth J]	RNA_pol_Rpb2_6_2nd_1	e3hkzJ3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RNA_pol_Rpb2_6_2nd_1	ECOD (1.6)
P [auth J]	RNA_pol_Rpb2_3	e3hkzJ4	A: a+b complex topology	X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_3	ECOD (1.6)
P [auth J]	RNA_pol_Rpb2_1	e3hkzJ7	A: a+b complex topology	X: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: insertion domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_1	ECOD (1.6)
P [auth J]	RNA_pol_Rpb2_45_1	e3hkzJ6	A: a+b complex topology	X: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: barrel domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_45_1	ECOD (1.6)
P [auth J]	RNA_pol_Rpb2_7	e3hkzJ2	A: a+b complex topology	X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: C-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_7	ECOD (1.6)
P [auth J]	RNA_pol_Rpb2_4	e3hkzJ5	A: a+b complex topology	X: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	H: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	T: inserted a+b domain in yeast RNA polymerase beta subunit	F: RNA_pol_Rpb2_4	ECOD (1.6)
C [auth B]	RNA_pol_Rpb2_6_3rd_2	e3hkzB3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_2	ECOD (1.6)
C [auth B]	RNA_pol_Rpb2_6_2nd_1	e3hkzB1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RNA_pol_Rpb2_6_2nd_1	ECOD (1.6)
C [auth B]	RNA_pol_Rpb2_3	e3hkzB7	A: a+b complex topology	X: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: N-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_3	ECOD (1.6)
C [auth B]	RNA_pol_Rpb2_1	e3hkzB2	A: a+b complex topology	X: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: insertion domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_1	ECOD (1.6)
C [auth B]	RNA_pol_Rpb2_45_1	e3hkzB4	A: a+b complex topology	X: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: barrel domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_45_1	ECOD (1.6)
C [auth B]	RNA_pol_Rpb2_7	e3hkzB5	A: a+b complex topology	X: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)	T: C-terminal domain in beta subunit of DNA dependent RNA-polymerase	F: RNA_pol_Rpb2_7	ECOD (1.6)
C [auth B]	RNA_pol_Rpb2_4	e3hkzB6	A: a+b complex topology	X: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	H: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)	T: inserted a+b domain in yeast RNA polymerase beta subunit	F: RNA_pol_Rpb2_4	ECOD (1.6)
O [auth M]	RNAP_A''	e3hkzM1	A: a+b two layers	X: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNAP_A''	ECOD (1.6)
O [auth M]	RNAP_II_Rpb1_C	e3hkzM2	A: a+b two layers	X: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNAP_II_Rpb1_C	ECOD (1.6)
O [auth M]	RNA_pol_Rpb1_5_3rd	e3hkzM4	A: a+b complex topology	X: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: central helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_5_3rd	ECOD (1.6)
O [auth M]	PRK04309_like_1	e3hkzM3	A: a+b complex topology	X: helical domain in yeast RNA-polymerases	H: third helical domain in yeast RNA-polymerase II beta-prime subunit (From Topology)	T: third helical domain in yeast RNA-polymerase II beta-prime subunit	F: PRK04309_like_1	ECOD (1.6)
B [auth C]	RNAP_A''	e3hkzC4	A: a+b two layers	X: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNAP_A''	ECOD (1.6)
B [auth C]	RNAP_II_Rpb1_C	e3hkzC3	A: a+b two layers	X: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	H: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)	T: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit	F: RNAP_II_Rpb1_C	ECOD (1.6)
B [auth C]	RNA_pol_Rpb1_5_3rd	e3hkzC2	A: a+b complex topology	X: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: central helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: central helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_5_3rd	ECOD (1.6)
B [auth C]	PRK04309_like_1	e3hkzC1	A: a+b complex topology	X: helical domain in yeast RNA-polymerases	H: third helical domain in yeast RNA-polymerase II beta-prime subunit (From Topology)	T: third helical domain in yeast RNA-polymerase II beta-prime subunit	F: PRK04309_like_1	ECOD (1.6)
Z	RNA_pol_Rpo13	e3hkzZ1	A: alpha bundles	X: YqgQ-like (From Topology)	H: YqgQ-like (From Topology)	T: YqgQ-like	F: RNA_pol_Rpo13	ECOD (1.6)
M [auth Y]	RNA_pol_Rpo13	e3hkzY1	A: alpha bundles	X: YqgQ-like (From Topology)	H: YqgQ-like (From Topology)	T: YqgQ-like	F: RNA_pol_Rpo13	ECOD (1.6)
Y [auth X]	DNA_RNApol_7kD	e3hkzX1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: DNA_RNApol_7kD	ECOD (1.6)
L [auth P]	DNA_RNApol_7kD	e3hkzP1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: DNA_RNApol_7kD	ECOD (1.6)
X [auth W]	RNA_pol_N	e3hkzW1	A: alpha arrays	X: HTH	H: RPB10 (From Topology)	T: RPB10	F: RNA_pol_N	ECOD (1.6)
K [auth N]	RNA_pol_N	e3hkzN1	A: alpha arrays	X: HTH	H: RPB10 (From Topology)	T: RPB10	F: RNA_pol_N	ECOD (1.6)
W [auth V]	RNA_pol_L_2	e3hkzV1	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L_2	ECOD (1.6)
J [auth L]	RNA_pol_L_2	e3hkzL1	A: a+b two layers	X: DCoH-like	H: RBP11-like subunits of RNA polymerase (From Topology)	T: RBP11-like subunits of RNA polymerase	F: RNA_pol_L_2	ECOD (1.6)
N [auth I]	RNA_pol_Rpb1_2	e3hkzI4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
N [auth I]	RNA_pol_Rpb1_1	e3hkzI3	A: a+b complex topology	X: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	H: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	T: N-terminal domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_1	ECOD (1.6)
N [auth I]	RNA_pol_Rpb1_4	e3hkzI2	A: a+b complex topology	X: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: second helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_4	ECOD (1.6)
N [auth I]	RNA_pol_Rpb1_3	e3hkzI1	A: a+b complex topology	X: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: first helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_3	ECOD (1.6)
A	RNA_pol_Rpb1_2	e3hkzA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
A	RNA_pol_Rpb1_1	e3hkzA4	A: a+b complex topology	X: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	H: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)	T: N-terminal domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_1	ECOD (1.6)
A	RNA_pol_Rpb1_4	e3hkzA3	A: a+b complex topology	X: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: second helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: second helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_4	ECOD (1.6)
A	RNA_pol_Rpb1_3	e3hkzA2	A: a+b complex topology	X: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	H: first helical domain in RNA-polymerase beta-prime subunit (From Topology)	T: first helical domain in RNA-polymerase beta-prime subunit	F: RNA_pol_Rpb1_3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
V [auth U]	3.90.940.10	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RNA polymerase subunit, RPB6/omega	CATH (4.2.0)
I [auth K]	3.90.940.10	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RNA polymerase subunit, RPB6/omega	CATH (4.2.0)
U [auth T]	3.90.940.20	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RPB5-like RNA polymerase subunit	CATH (4.2.0)
H	3.90.940.20	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RPB5-like RNA polymerase subunit	CATH (4.2.0)
T [auth S]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.2.0)
G	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.2.0)
S [auth R]	6.10.140.930	Special	Helix non-globular	Helix Hairpins		CATH (4.2.0)
S [auth R]	1.10.150.80	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.2.0)
F	6.10.140.930	Special	Helix non-globular	Helix Hairpins		CATH (4.2.0)
F	1.10.150.80	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.2.0)
E	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.2.0)
E	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.2.0)
R [auth Q]	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.2.0)
R [auth Q]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.2.0)
Q [auth O]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.2.0)
Q [auth O]	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.2.0)
Q [auth O]	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.2.0)
D	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.2.0)
D	2.170.120.12	Mainly Beta	Beta Complex	RNA Polymerase Alpha Subunit	Chain A, domain 2	CATH (4.2.0)
D	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.2.0)
P [auth J]	3.90.1110.10	Alpha Beta	Alpha-Beta Complex	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.2.0)
P [auth J]	3.90.1070.20	Alpha Beta	Alpha-Beta Complex	Hypothetical Protein Ta0175	Chain: A, domain 2	CATH (4.2.0)
P [auth J]	2.40.270.10	Mainly Beta	Beta Barrel	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.2.0)
P [auth J]	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.2.0)
P [auth J]	3.90.1800.10	Alpha Beta	Alpha-Beta Complex	DCoH-like	RNA polymerase alpha subunit dimerisation domain	CATH (4.2.0)
C [auth B]	3.90.1110.10	Alpha Beta	Alpha-Beta Complex	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.2.0)
C [auth B]	3.90.1070.20	Alpha Beta	Alpha-Beta Complex	Hypothetical Protein Ta0175	Chain: A, domain 2	CATH (4.2.0)
C [auth B]	2.40.270.10	Mainly Beta	Beta Barrel	Dna-directed Rna Polymerase Ii 140kd Polypeptide	Chain: B	CATH (4.2.0)
C [auth B]	2.40.50.150	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II, Rpb2 subunit, wall domain	CATH (4.2.0)
C [auth B]	3.90.1800.10	Alpha Beta	Alpha-Beta Complex	DCoH-like	RNA polymerase alpha subunit dimerisation domain	CATH (4.2.0)
O [auth M]	1.10.150.390	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.2.0)
B [auth C]	1.10.150.390	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.2.0)
Z	6.20.450.10	Special	Other non-globular	DNA Excision Repair, Uvrb	Chain A	CATH (4.2.0)
M [auth Y]	6.20.450.10	Special	Other non-globular	DNA Excision Repair, Uvrb	Chain A	CATH (4.2.0)
Y [auth X]	2.20.28.30	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	RNA polymerase ii, chain L	CATH (4.2.0)
L [auth P]	2.20.28.30	Mainly Beta	Single Sheet	Rubrerythrin, domain 2	RNA polymerase ii, chain L	CATH (4.2.0)
X [auth W]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.2.0)
K [auth N]	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.2.0)
W [auth V]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.2.0)
J [auth L]	3.30.1360.10	Alpha Beta	2-Layer Sandwich	Gyrase A	domain 2	CATH (4.2.0)
N [auth I]	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.2.0)
N [auth I]	3.30.1490.180	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.2.0)
N [auth I]	1.10.10.1950	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.2.0)
N [auth I]	4.10.320.40	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase		CATH (4.2.0)
N [auth I]	2.60.40.2940	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.2.0)
N [auth I]	1.10.132.30	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.2.0)
N [auth I]	6.10.250.2940	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.2.0)
N [auth I]	6.20.50.80	Special	Other non-globular	N-terminal domain of TfIIb		CATH (4.2.0)
A	2.40.40.20	Mainly Beta	Beta Barrel	Barwin-like endoglucanases		CATH (4.2.0)
A	3.30.1490.180	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.2.0)
A	1.10.10.1950	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A		CATH (4.2.0)
A	4.10.320.40	Few Secondary Structures	Irregular	Dihydrolipoamide Transferase		CATH (4.2.0)
A	2.60.40.2940	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.2.0)
A	1.10.132.30	Mainly Alpha	Orthogonal Bundle	Topoisomerase I	Chain A, domain 4	CATH (4.2.0)
A	6.10.250.2940	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.2.0)
A	6.20.50.80	Special	Other non-globular	N-terminal domain of TfIIb		CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth K], V [auth U]	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
H, U [auth T]	PF01191	RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C)	RNA polymerase Rpb5, C-terminal domain	The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.	Domain
G, T [auth S]	PF16992	DNA-directed RNA polymerase, subunit G (RNA_pol_RpbG)	DNA-directed RNA polymerase, subunit G	-	Family
F, S [auth R]	PF03874	RNA polymerase Rpb4 (RNA_pol_Rpb4)	RNA polymerase Rpb4	-	Family
E, R [auth Q]	PF03876	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N)	SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397	Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ...	Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3].	Domain
E, R [auth Q]	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain
D, Q [auth O]	PF01193	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.	Domain
D, Q [auth O]	PF01000	RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)	RNA polymerase Rpb3/RpoA insert domain	Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal	Domain
C [auth B], P [auth J]	PF04561	RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)	RNA polymerase Rpb2, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA po ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).	Domain
C [auth B], P [auth J]	PF04560	RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)	RNA polymerase Rpb2, domain 7	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].	Domain
C [auth B], P [auth J]	PF04565	RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)	RNA polymerase Rpb2, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1].	Domain
C [auth B], P [auth J]	PF04566	RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4)	RNA polymerase Rpb2, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 4, is also known as the external 2 domain [1].	Domain
C [auth B], P [auth J]	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
C [auth B], P [auth J]	PF00562	RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)	RNA polymerase Rpb2, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).	Domain
C [auth B], P [auth J]	PF04567	RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5)	RNA polymerase Rpb2, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain [1].	Domain
B [auth C], O [auth M]	PF04998	RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)	RNA polymerase Rpb1, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].	Domain
K [auth N], X [auth W]	PF01194	RNA polymerases N / 8 kDa subunit (RNA_pol_N)	RNA polymerases N / 8 kDa subunit		Domain
J [auth L], W [auth V]	PF13656	RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2)	RNA polymerase Rpb3/Rpb11 dimerisation domain	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...	The two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11.	Domain
A, N [auth I]	PF00623	RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)	RNA polymerase Rpb1, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].	Domain
A, N [auth I]	PF05000	RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)	RNA polymerase Rpb1, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].	Domain
A, N [auth I]	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
A, N [auth I]	PF04998	RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)	RNA polymerase Rpb1, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
I [auth K], V [auth U]	DNA-directed RNA polymerase subunit K	DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process transcription by RNA polymerase I metabolic process cellular process macromolecule metabolic process tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III transcription by RNA polymerase III transcription by RNA polymerase II	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
H, U [auth T]	DNA-directed RNA polymerase subunit H	DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
G, T [auth S]	DNA-directed RNA polymerase, subunit G (RpoG)	DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
F, S [auth R]	DNA-directed RNA polymerase, subunit F (RpoF)	binding nucleoside phosphate binding nucleotide binding heterocyclic compound binding small molecule binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
E, R [auth Q]	DNA-directed RNA polymerase, subunit E' (RpoE1)	DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription initiation nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
D, Q [auth O]	DNA-directed RNA polymerase subunit D	DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups iron-sulfur cluster binding 3 iron, 4 sulfur cluster binding DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups iron-sulfur cluster binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding protein binding protein dimerization activity cation binding ion binding metal ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
C [auth B], P [auth J]	DNA-directed RNA polymerase subunit B	DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding nucleoside binding DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
B [auth C], O [auth M]	DNA-directed RNA polymerase subunit A''	DNA binding binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
M [auth Y], Z	DNA-directed RNA polymerase subunit 13	DNA binding binding nucleic acid binding transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	-	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
L [auth P], Y [auth X]	DNA-directed RNA polymerase subunit P	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
K [auth N], X [auth W]	DNA-directed RNA polymerase subunit N	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
J [auth L], W [auth V]	DNA-directed RNA polymerase subunit L	DNA binding binding nucleic acid binding protein binding protein dimerization activity DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex
A, N [auth I]	DNA-directed RNA polymerase subunit A'	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding DNA binding nucleic acid binding DNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups transition metal ion binding zinc ion binding	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex RNA polymerase complex DNA-directed RNA polymerase complex transferase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth K], V [auth U]	IPR020708	DNA-directed RNA polymerase, 14-18kDa subunit, conserved site	Conserved Site
I [auth K], V [auth U]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
I [auth K], V [auth U]	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
I [auth K], V [auth U]	IPR006111	Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit	Family
H, U [auth T]	IPR014381	DNA-directed RNA polymerase subunit Rpo5/Rpb5	Family
H, U [auth T]	IPR035913	RPB5-like RNA polymerase subunit superfamily	Homologous Superfamily
H, U [auth T]	IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	Domain
H, U [auth T]	IPR020608	RNA polymerase, subunit H/Rpb5, conserved site	Conserved Site
G, T [auth S]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
G, T [auth S]	IPR031555	DNA-directed RNA polymerase subunit Rpo8	Family
F, S [auth R]	IPR005574	RNA polymerase subunit Rpb4/RPC9	Family
F, S [auth R]	IPR044876	HRDC domain superfamily	Homologous Superfamily
F, S [auth R]	IPR010997	HRDC-like superfamily	Homologous Superfamily
F, S [auth R]	IPR010924	DNA-directed RNA polymerase subunit Rpo4	Family
E, R [auth Q]	IPR046399	DNA-directed RNA polymerase subunit Rpo7	Family
E, R [auth Q]	IPR036898	RNA polymerase Rpb7-like, N-terminal domain superfamily	Homologous Superfamily
E, R [auth Q]	IPR004519	DNA-directed RNA polymerase, subunit E/RPC8	Family
E, R [auth Q]	IPR003029	S1 domain	Domain
E, R [auth Q]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
E, R [auth Q]	IPR045113	RNA polymerase subunit Rpb7-like	Family
E, R [auth Q]	IPR005576	RNA polymerase Rpb7-like , N-terminal	Domain
D, Q [auth O]	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
D, Q [auth O]	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
D, Q [auth O]	IPR050518	Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase Subunit	Family
D, Q [auth O]	IPR022842	DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1	Family
D, Q [auth O]	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
D, Q [auth O]	IPR001514	DNA-directed RNA polymerase, 30-40kDa subunit, conserved site	Conserved Site
D, Q [auth O]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
C [auth B], P [auth J]	IPR007642	RNA polymerase Rpb2, domain 2	Domain
C [auth B], P [auth J]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
C [auth B], P [auth J]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
C [auth B], P [auth J]	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
C [auth B], P [auth J]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
C [auth B], P [auth J]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
C [auth B], P [auth J]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
C [auth B], P [auth J]	IPR007646	RNA polymerase Rpb2, domain 4	Domain
C [auth B], P [auth J]	IPR007647	RNA polymerase Rpb2, domain 5	Domain
C [auth B], P [auth J]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
C [auth B], P [auth J]	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
C [auth B], P [auth J]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
C [auth B], P [auth J]	IPR019969	DNA-directed RNA polymerase subunit Rpo2	Family
B [auth C], O [auth M]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
B [auth C], O [auth M]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
B [auth C], O [auth M]	IPR012757	DNA-directed RNA polymerase subunit Rpo1C	Family
M [auth Y], Z	IPR021985	RNA polymerase Rpo13 subunit HTH domain	Domain
L [auth P], Y [auth X]	IPR006591	RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4	Family
L [auth P], Y [auth X]	IPR023464	DNA-directed RNA polymerase subunit Rpo12	Family
L [auth P], Y [auth X]	IPR029040	RNA polymerase subunit RPABC4/transcription elongation factor Spt4	Homologous Superfamily
K [auth N], X [auth W]	IPR023580	RNA polymerase subunit RPB10	Homologous Superfamily
K [auth N], X [auth W]	IPR020789	RNA polymerases, subunit N, zinc binding site	Binding Site
K [auth N], X [auth W]	IPR000268	DNA-directed RNA polymerase subunit RPABC5/Rpb10	Family
J [auth L], W [auth V]	IPR022905	DNA-directed RNA polymerase subunit Rpo11-like	Family
J [auth L], W [auth V]	IPR009025	DNA-directed RNA polymerase, RBP11-like dimerisation domain	Domain
J [auth L], W [auth V]	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily
J [auth L], W [auth V]	IPR008193	DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site	Conserved Site
A, N [auth I]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
A, N [auth I]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
A, N [auth I]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
A, N [auth I]	IPR012758	DNA-directed RNA polymerase subunit Rpo1N	Family
A, N [auth I]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
A, N [auth I]	IPR000722	RNA polymerase, alpha subunit	Domain
A, N [auth I]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
A, N [auth I]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
A, N [auth I]	IPR006592	RNA polymerase, N-terminal	Domain
A, N [auth I]	IPR007080	RNA polymerase Rpb1, domain 1	Domain

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The X-ray crystal structure of RNA polymerase from Archaea

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

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