4XLS | pdb_00004xls

Crystal structure of T. aquaticus transcription initiation complex with CarD containing upstream fork promoter.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
L	SCOP2B Superfamily	Sigma factor domain-like	8040679	3000953	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8044411	3001393	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Sigma factor domain-like	8044410	3000953	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sigma factor domain-like	8044410	3000953	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sigma factor domain-like	8040679	3000953	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sigma2 domain of RNA polymerase sigma factors	8044411	3001393	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	RPB6/omega subunit-like	8034762	3000189	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RPB6/omega subunit-like	8034762	3000189	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8032539	3001330	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8032539	3001330	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8032536	3001330	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8032536	3001330	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8032536	3001330	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Two-barrel nucleic acid polymerases	8032536	3001330	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8034760	3001500	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8034760	3001500	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8034760	3001500	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	3001655	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Insert subdomain of RNA polymerase alpha subunit	8034760	3001500	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RBP11-like subunits of RNA polymerase	8034759	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)
N	CarD_CdnL_TRCF	e4xlsN1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: CarD_CdnL_TRCF	ECOD (1.6)
N	CdnL	e4xlsN2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: CdnL	ECOD (1.6)
M	CarD_CdnL_TRCF	e4xlsM1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: CarD_CdnL_TRCF	ECOD (1.6)
M	CdnL	e4xlsM2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: CdnL	ECOD (1.6)
L	Sigma70_r3	e4xlsL1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r3	ECOD (1.6)
L	Sigma70_r4	e4xlsL3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4	ECOD (1.6)
L	Sigma70_r2_2	e4xlsL2	A: alpha complex topology	X: Sigma2 domain-like	H: Sigma2 domain of RNA polymerase sigma factors (From Topology)	T: Sigma2 domain of RNA polymerase sigma factors	F: Sigma70_r2_2	ECOD (1.6)
F	Sigma70_r3	e4xlsF3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r3	ECOD (1.6)
F	Sigma70_r4	e4xlsF1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Sigma70_r4	ECOD (1.6)
F	Sigma70_r2_2	e4xlsF2	A: alpha complex topology	X: Sigma2 domain-like	H: Sigma2 domain of RNA polymerase sigma factors (From Topology)	T: Sigma2 domain of RNA polymerase sigma factors	F: Sigma70_r2_2	ECOD (1.6)
K	RNA_pol_Rpb6	e4xlsK1	A: alpha arrays	X: RPB6/omega subunit-like (From Homology)	H: RPB6/omega subunit-like	T: RNA polymerase omega subunit	F: RNA_pol_Rpb6	ECOD (1.6)
E	RNA_pol_Rpb6	e4xlsE1	A: alpha arrays	X: RPB6/omega subunit-like (From Homology)	H: RPB6/omega subunit-like	T: RNA polymerase omega subunit	F: RNA_pol_Rpb6	ECOD (1.6)
J	RNA_pol_Rpb1_2	e4xlsJ2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
J	PRK00566_1st	e4xlsJ6	A: alpha arrays	X: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology)	H: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology)	T: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit	F: PRK00566_1st	ECOD (1.6)
J	PRK00566_2nd	e4xlsJ5	A: a+b two layers	X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: PRK00566_2nd	ECOD (1.6)
J	biotinyl_domain_like	e4xlsJ1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: biotinyl_domain_like	ECOD (1.6)
J	RnfC_N_like_1	e4xlsJ3	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RnfC_N_like_1	ECOD (1.6)
J	RNA_pol_Rpb1_5_2nd	e4xlsJ4	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_Rpb1_5_2nd	ECOD (1.6)
J	RNA_pol_Rpb1_1	e4xlsJ10	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)
J	RNA_pol_Rpb1_5_3rd	e4xlsJ8	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)
J	RNA_pol_Rpb1_4	e4xlsJ9	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)
J	RNA_pol_Rpb1_3	e4xlsJ7	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)
D	RNA_pol_Rpb1_2	e4xlsD2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb1_2	ECOD (1.6)
D	PRK00566_1st	e4xlsD12	A: alpha arrays	X: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology)	H: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit (From Topology)	T: inserted helical subdomain in bacterial RNA-polymerase beta-prime subunit	F: PRK00566_1st	ECOD (1.6)
D	PRK00566_2nd	e4xlsD7	A: a+b two layers	X: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: PRK00566_2nd	ECOD (1.6)
D	PRK00566_like	e4xlsD11	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Duplicated hybrid motif	F: PRK00566_like	ECOD (1.6)
D	biotinyl_domain_like	e4xlsD10	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: biotinyl_domain_like	ECOD (1.6)
D	RnfC_N_like_1	e4xlsD8	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: RnfC_N_like_1	ECOD (1.6)
D	RNA_pol_Rpb1_5_2nd	e4xlsD1	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_Rpb1_5_2nd	ECOD (1.6)
D	Biotin_lipoyl_2_like	e4xlsD5	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: Biotin_lipoyl_2_like	ECOD (1.6)
D	RNA_pol_Rpb1_1	e4xlsD3	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)
D	RNA_pol_Rpb1_5_3rd	e4xlsD4	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)
D	RNA_pol_Rpb1_4	e4xlsD6	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)
D	RNA_pol_Rpb1_3	e4xlsD9	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)
I	RNA_pol_Rpb2_6_3rd_3	e4xlsI6	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_3	ECOD (1.6)
I	RNA_pol_Rpb2_6_1st_1	e4xlsI4	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_1st_1	ECOD (1.6)
I	RNA_pol_Rpb2_6_2nd	e4xlsI3	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	ECOD (1.6)
I	RNA_pol_Rpb2_3	e4xlsI7	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)
I	RNA_pol_Rpb2_1	e4xlsI1	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)
I	RNA_pol_Rpb2_45	e4xlsI2	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	ECOD (1.6)
I	RNA_pol_Rpb2_7	e4xlsI5	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	RNA_pol_Rpb2_6_3rd_3	e4xlsC3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: double psi	F: RNA_pol_Rpb2_6_3rd_3	ECOD (1.6)
C	RNA_pol_Rpb2_6_1st_1	e4xlsC5	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_1st_1	ECOD (1.6)
C	RNA_pol_Rpb2_6_2nd	e4xlsC6	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	ECOD (1.6)
C	RNA_pol_Rpb2_3	e4xlsC1	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	RNA_pol_Rpb2_1	e4xlsC7	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	RNA_pol_Rpb2_45	e4xlsC2	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	ECOD (1.6)
C	RNA_pol_Rpb2_7	e4xlsC4	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)
H	RNA_pol_L	e4xlsH2	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)
H	RNA_pol_A_bac	e4xlsH1	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	ECOD (1.6)
G	RNA_pol_L	e4xlsG2	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)
G	RNA_pol_A_bac	e4xlsG1	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	ECOD (1.6)
B	RNA_pol_L	e4xlsB2	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)
B	RNA_pol_A_bac	e4xlsB1	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	ECOD (1.6)
A	RNA_pol_L	e4xlsA2	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)
A	RNA_pol_A_bac	e4xlsA1	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	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
M, N	PF02559	CarD-like/TRCF RID domain (CarD_TRCF_RID)	CarD-like/TRCF RID domain	This is the RNA polymerase interacting domain (RID) of transcription-repair-coupling factor (TRCF), CarD and CarD homologue in Myxococcus xanthus, called CdnL. In Myxococcus xanthus, CdnL is a protein required for the activation of light- and starvat ...	This is the RNA polymerase interacting domain (RID) of transcription-repair-coupling factor (TRCF), CarD and CarD homologue in Myxococcus xanthus, called CdnL. In Myxococcus xanthus, CdnL is a protein required for the activation of light- and starvation-inducible genes [1]. It interacts with the zinc-binding protein CarG to form a complex that regulates multiple processes in Myxococcus xanthus [4]. CarD is widely distributed among bacteria and represents a distinct class of RNAP binding proteins that regulate transcription and essential processes [4-8]. TRCF displaces RNA polymerase stalled at a lesion, binds to the damage recognition protein UvrA, and increases the template strand repair rate during transcription [3].	Domain
M, N	PF21095	CarD, C-terminal domain (CarD_C)	CarD, C-terminal domain	This entry represents the C-terminal helical domain of CarD from Mycobacterium tuberculosis, a RNAP-binding protein that regulates transcription and essential processes [1-3]. This domain binds DNA in a non-specific manner [4].	Domain
F, L	PF04539	Sigma-70 region 3 (Sigma70_r3)	Sigma-70 region 3	-	Family
F, L	PF00140	Sigma-70 factor, region 1.2 (Sigma70_r1_2)	Sigma-70 factor, region 1.2	-	Family
F, L	PF04542	Sigma-70 region 2 (Sigma70_r2)	Sigma-70 region 2	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA ...	Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA polymerase binding determinant. The core binding helix, interacts with the clamp domain of the largest polymerase subunit, beta prime [1,2]. The aromatic residues of the recognition helix, found at the C-terminus of this domain are though to mediate strand separation, thereby allowing transcription initiation [1,2].	Domain
F, L	PF04545	Sigma-70, region 4 (Sigma70_r4)	Sigma-70, region 4	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix fami ...	Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.	Domain
E, K	PF01192	RNA polymerase Rpb6 (RNA_pol_Rpb6)	RNA polymerase Rpb6	-	Family
D, J	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
D, J	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
D, J	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
D, J	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
D, J	PF21668	DNA-directed RNA polymerase subunit beta', hybrid domain (RPOC_hybrid)	DNA-directed RNA polymerase subunit beta', hybrid domain	This is a hybrid domain found in DNA-directed RNA polymerase subunit beta' (RPOC) found in Deinococcus [1-5].	Domain
D, J	PF04997	RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)	RNA polymerase Rpb1, domain 1	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 1, represents the clamp dom ...	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 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].	Domain
C, I	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, I	PF10385	RNA polymerase beta subunit external 1 domain (RNA_pol_Rpb2_45)	RNA polymerase beta subunit external 1 domain	RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between ...	RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region [1].	Domain
C, I	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, I	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, I	PF04563	RNA polymerase beta subunit (RNA_pol_Rpb2_1)	RNA polymerase beta subunit	-	Family
C, I	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
A, B, G, H	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
A, B, G, H	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
P, R [auth S]	DNA (5'-D(PGPCPAPCPAPAPTPTPTPAPAPCPAPCPTPTPTPTPGPTPCPAPAPG)-3')	-	-	-
O, Q [auth R]	DNA (30-MER)	-	-	-
M, N	CarD-like transcriptional regulator	-	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process rRNA transcription metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process rRNA transcription metabolic process cellular process macromolecule metabolic process rRNA metabolic process	-
F, L	RNA polymerase sigma factor SigA	DNA binding binding nucleic acid binding transcription regulator activity DNA-binding transcription factor activity sigma factor activity	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
E, K	DNA-directed RNA polymerase subunit omega	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	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, J	DNA-directed RNA polymerase subunit beta'	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	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, I	DNA-directed RNA polymerase subunit beta	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	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	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, B, G, H	DNA-directed RNA polymerase subunit alpha	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
M, N	IPR042215	CarD-like, C-terminal domain	Homologous Superfamily
M, N	IPR048792	CarD, C-terminal domain	Domain
M, N	IPR052531	CarD-like transcription regulator	Family
M, N	IPR036101	CarD-like/TRCF, RNAP-interacting domain superfamily	Homologous Superfamily
M, N	IPR003711	CarD-like/TRCF, RNAP-interacting domain	Domain
F, L	IPR007627	RNA polymerase sigma-70 region 2	Domain
F, L	IPR000943	RNA polymerase sigma-70	Domain
F, L	IPR013325	RNA polymerase sigma factor, region 2	Homologous Superfamily
F, L	IPR013324	RNA polymerase sigma factor, region 3/4-like	Homologous Superfamily
F, L	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
F, L	IPR012760	RNA polymerase sigma factor RpoD, C-terminal	Domain
F, L	IPR009042	RNA polymerase sigma-70 region 1.2	Domain
F, L	IPR007630	RNA polymerase sigma-70 region 4	Domain
F, L	IPR014284	RNA polymerase sigma-70-like domain	Domain
F, L	IPR007624	RNA polymerase sigma-70 region 3	Domain
F, L	IPR028630	RNA polymerase sigma factor RpoD	Family
F, L	IPR050239	Sigma-70 factor family, RNA polymerase initiation factors	Family
E, K	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
E, K	IPR003716	DNA-directed RNA polymerase, omega subunit	Family
E, K	IPR006110	RNA polymerase, subunit omega/Rpo6/RPB6	Family
D, J	IPR007066	RNA polymerase Rpb1, domain 3	Domain
D, J	IPR007081	RNA polymerase Rpb1, domain 5	Domain
D, J	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
D, J	IPR012754	DNA-directed RNA polymerase, subunit beta-prime, bacterial type	Family
D, J	IPR048566	DNA-directed RNA polymerase subunit beta', hybrid domain	Domain
D, J	IPR042102	RNA polymerase Rpb1, domain 3 superfamily	Homologous Superfamily
D, J	IPR007083	RNA polymerase Rpb1, domain 4	Domain
D, J	IPR000722	RNA polymerase, alpha subunit	Domain
D, J	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
D, J	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
D, J	IPR006592	RNA polymerase, N-terminal	Domain
D, J	IPR007080	RNA polymerase Rpb1, domain 1	Domain
C, I	IPR007642	RNA polymerase Rpb2, domain 2	Domain
C, I	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
C, I	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
C, I	IPR042107	DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily	Homologous Superfamily
C, I	IPR037034	RNA polymerase Rpb2, domain 2 superfamily	Homologous Superfamily
C, I	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
C, I	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
C, I	IPR007645	RNA polymerase Rpb2, domain 3	Domain
C, I	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
C, I	IPR019462	DNA-directed RNA polymerase, beta subunit, external 1 domain	Domain
C, I	IPR010243	DNA-directed RNA polymerase beta subunit, bacterial-type	Family
C, I	IPR007644	RNA polymerase, beta subunit, protrusion	Domain
C, I	IPR007641	RNA polymerase Rpb2, domain 7	Domain
A, B, G, H	IPR011773	DNA-directed RNA polymerase, alpha subunit	Family
A, B, G, H	IPR011262	DNA-directed RNA polymerase, insert domain	Domain
A, B, G, H	IPR011260	RNA polymerase, alpha subunit, C-terminal	Domain
A, B, G, H	IPR011263	DNA-directed RNA polymerase, RpoA/D/Rpb3-type	Domain
A, B, G, H	IPR036643	DNA-directed RNA polymerase, insert domain superfamily	Homologous Superfamily
A, B, G, H	IPR036603	RNA polymerase, RBP11-like subunit	Homologous Superfamily