1H38 | pdb_00001h38

Structure of a T7 RNA polymerase elongation complex at 2.9A resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1h38a_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	T7 RNA polymerase	T7 RNA polymerase	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
B	d1h38b_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	T7 RNA polymerase	T7 RNA polymerase	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
C	d1h38c_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	T7 RNA polymerase	T7 RNA polymerase	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)
D	d1h38d_	Multi-domain proteins (alpha and beta)	DNA/RNA polymerases	DNA/RNA polymerases	T7 RNA polymerase	T7 RNA polymerase	(Escherichia phage T7 ) [TaxId: 10760 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Nucleotide cyclase/DNA polymerase palm domain-like	8037503	3001272	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)
A	HHH_5	e1h38A1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: HHH_5	ECOD (v294.1)
A	RNase_P_Rpp14	e1h38A5	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
A	Flu_PB2_5th	e1h38A2	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: Flu_PB2_5th	ECOD (v294.1)
B	HHH_5	e1h38B1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: HHH_5	ECOD (v294.1)
B	RNase_P_Rpp14	e1h38B5	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
B	Flu_PB2_5th	e1h38B2	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: Flu_PB2_5th	ECOD (v294.1)
C	HHH_5	e1h38C1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: HHH_5	ECOD (v294.1)
C	RNase_P_Rpp14	e1h38C5	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
C	Flu_PB2_5th	e1h38C2	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: Flu_PB2_5th	ECOD (v294.1)
D	HHH_5	e1h38D1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: YozE-like	T: YozE-like	F: HHH_5	ECOD (v294.1)
D	RNase_P_Rpp14	e1h38D5	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: RNase_P_Rpp14	ECOD (v294.1)
D	Flu_PB2_5th	e1h38D2	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: ADP-ribosylation	T: ADP-ribosylation	F: Flu_PB2_5th	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.1320.10	Mainly Alpha	Orthogonal Bundle	T7 RNA polymerase	domain 1	CATH (4.3.0)
A	1.10.287.260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
A	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	1.10.287.280	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B	1.10.1320.10	Mainly Alpha	Orthogonal Bundle	T7 RNA polymerase	domain 1	CATH (4.3.0)
B	1.10.287.260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
B	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	1.10.287.280	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
B	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
C	1.10.1320.10	Mainly Alpha	Orthogonal Bundle	T7 RNA polymerase	domain 1	CATH (4.3.0)
C	1.10.287.260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
C	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C	1.10.287.280	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
C	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
D	1.10.1320.10	Mainly Alpha	Orthogonal Bundle	T7 RNA polymerase	domain 1	CATH (4.3.0)
D	1.10.287.260	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
D	3.30.70.370	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D	1.10.287.280	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
D	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF14700	DNA-directed RNA polymerase N-terminal (RPOL_N)	DNA-directed RNA polymerase N-terminal	This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme [1]. In order to make mRNA transcripts the ...	This is the N-terminal domain of DNA-directed RNA polymerase. This domain has a role in interaction with regions of upstream promoter DNA and the nascent RNA chain, leading to the processivity of the enzyme [1]. In order to make mRNA transcripts the RNA polymerase undergoes a transition from the initiation phase (which only makes short fragments of RNA) to an elongation phase. This domain undergoes a structural change in the transition from initiation to elongation phase. The structural change results in abolition of the promoter binding site, creation of a channel accommodating the heteroduplex in the active site and formation of an exit tunnel which the RNA transcript passes through after peeling off the heteroduplex [2].	Domain
A, B, C, D	PF00940	DNA-dependent RNA polymerase (RNA_pol)	DNA-dependent RNA polymerase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	DNA-DIRECTED RNA POLYMERASE	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	viral gene expression DNA-templated viral transcription viral process viral transcription 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 viral gene expression DNA-templated viral transcription viral process viral transcription 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
E, H, K, N	5'-D(GPGPGPAPAPTPCPGPAPCP APTPCPGPCPCPGPC)-3'	-	-	-
F, I, L, O	5'-R(APAPCPUPGPCPGPGPCPGP APU)-3'	-	-	-
G, J, M, P	5'-D(GPTPCPGPAPTPTPCPCPCP)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR029262	DNA-directed RNA polymerase, N-terminal	Domain
A, B, C, D	IPR002092	DNA-directed RNA polymerase, phage-type	Family
A, B, C, D	IPR024075	DNA-directed RNA polymerase, helix hairpin domain superfamily	Homologous Superfamily
A, B, C, D	IPR046950	DNA-directed RNA polymerase, C-terminal domain, phage-type	Domain
A, B, C, D	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D	IPR037159	DNA-directed RNA polymerase, N-terminal domain superfamily	Homologous Superfamily