1GO3

Structure of an archeal homolog of the eukaryotic RNA polymerase II RPB4/RPB7 complex

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 [auth E]	d1go3e1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
A [auth E]	d1go3e2	Alpha and beta proteins (a+b)	Dodecin subunit-like	N-terminal, heterodimerisation domain of RBP7 (RpoE)	N-terminal, heterodimerisation domain of RBP7 (RpoE)	N-terminal, heterodimerisation domain of RBP7 (RpoE)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C [auth M]	d1go3m1	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	C-terminal domain of RNA polymerase II subunit RBP7 (RpoE)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C [auth M]	d1go3m2	Alpha and beta proteins (a+b)	Dodecin subunit-like	N-terminal, heterodimerisation domain of RBP7 (RpoE)	N-terminal, heterodimerisation domain of RBP7 (RpoE)	N-terminal, heterodimerisation domain of RBP7 (RpoE)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
B [auth F]	d1go3f_	All alpha proteins	SAM domain-like	HRDC-like	RNA polymerase II subunit RBP4 (RpoF)	RNA polymerase II subunit RBP4 (RpoF)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
D [auth N]	d1go3n_	All alpha proteins	SAM domain-like	HRDC-like	RNA polymerase II subunit RBP4 (RpoF)	RNA polymerase II subunit RBP4 (RpoF)	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth E]	SCOP2 Family	Cold shock DNA-binding domain-like	8032020	4001909	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Family	N-terminal heterodimerisation domain of RBP7 (RpoE)	8032021	4003624	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Superfamily	Nucleic acid-binding proteins	8044398	3000135	SCOP2 (2022-06-29)
A [auth E]	SCOP2 Superfamily	N-terminal heterodimerisation domain of RBP7 (RpoE)	8044399	3001137	SCOP2 (2022-06-29)
C [auth M]	SCOP2B Superfamily	N-terminal heterodimerisation domain of RBP7 (RpoE)	8044399	3001137	SCOP2B (2022-06-29)
C [auth M]	SCOP2B Superfamily	Nucleic acid-binding proteins	8044398	3000135	SCOP2B (2022-06-29)
B [auth F]	SCOP2 Family	RNA polymerase II subunit RBP4 (RpoF)	8023718	4002844	SCOP2 (2022-06-29)
B [auth F]	SCOP2 Superfamily	HRDC-like	8036098	3000132	SCOP2 (2022-06-29)
D [auth N]	SCOP2B Superfamily	HRDC-like	8036098	3000132	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 [auth E]	S1_1	e1go3E1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
A [auth E]	SHS2_Rpb7-N	e1go3E2	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)
C [auth M]	S1_1	e1go3M1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
C [auth M]	SHS2_Rpb7-N	e1go3M2	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)
B [auth F]	RNA_pol_Rpb4	e1go3F1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: RNA_pol_Rpb4	ECOD (1.6)
D [auth N]	RNA_pol_Rpb4	e1go3N1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: RNA_pol_Rpb4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth E]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A [auth E]	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
C [auth M]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C [auth M]	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B [auth F]	1.10.150.80	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
B [auth F]	6.10.140.10	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)
D [auth N]	1.10.150.80	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
D [auth N]	6.10.140.10	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E], C [auth M]	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
A [auth E], C [auth M]	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
B [auth F], D [auth N]	PF03874	RNA polymerase Rpb4 (RNA_pol_Rpb4)	RNA polymerase Rpb4	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], C [auth M]	DNA-DIRECTED RNA POLYMERASE SUBUNIT E	DNA binding binding organic cyclic compound binding nucleic acid binding DNA-directed 5'-3' 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	cellular biosynthetic process cellular metabolic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process cellular biosynthetic process cellular metabolic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity 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 F], D [auth N]	DNA-DIRECTED RNA POLYMERASE SUBUNIT F	binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding DNA-directed 5'-3' 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 binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding small molecule binding DNA-directed 5'-3' 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	cellular biosynthetic process cellular metabolic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process cellular biosynthetic process cellular metabolic 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 organic cyclic compound metabolic process nucleic acid biosynthetic process organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process cellular process macromolecule metabolic process	intracellular anatomical structure cytoplasm cellular anatomical entity 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
A [auth E], C [auth M]	IPR046399	DNA-directed RNA polymerase subunit Rpo7	Family
A [auth E], C [auth M]	IPR036898	RNA polymerase Rpb7-like, N-terminal domain superfamily	Homologous Superfamily
A [auth E], C [auth M]	IPR004519	DNA-directed RNA polymerase, subunit E/RPC8	Family
A [auth E], C [auth M]	IPR003029	S1 domain	Domain
A [auth E], C [auth M]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A [auth E], C [auth M]	IPR045113	RNA polymerase subunit Rpb7-like	Family
A [auth E], C [auth M]	IPR005576	RNA polymerase Rpb7-like , N-terminal	Domain
B [auth F], D [auth N]	IPR005574	RNA polymerase subunit Rpb4/RPC9	Family
B [auth F], D [auth N]	IPR044876	HRDC domain superfamily	Homologous Superfamily
B [auth F], D [auth N]	IPR010997	HRDC-like superfamily	Homologous Superfamily
B [auth F], D [auth N]	IPR010924	DNA-directed RNA polymerase subunit Rpo4	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.