1Y14

Crystal structure of yeast subcomplex of Rpb4 and Rpb7

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)
B	d1y14b1	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)	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1y14b2	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)	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d1y14d1	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)	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d1y14d2	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)	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1y14a_	All alpha proteins	SAM domain-like	HRDC-like	RNA polymerase II subunit RBP4 (RpoF)	RNA polymerase II subunit RBP4 (RpoF)	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1y14c_	All alpha proteins	SAM domain-like	HRDC-like	RNA polymerase II subunit RBP4 (RpoF)	RNA polymerase II subunit RBP4 (RpoF)	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Nucleic acid-binding proteins	8044251	3000135	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	N-terminal, heterodimerisation domain of RBP7 (RpoE)	8044252	3001137	SCOP2B (2022-06-29)
D	SCOP2 Family	Cold shock DNA-binding domain-like	8031873	4001909	SCOP2 (2022-06-29)
D	SCOP2 Family	N-terminal, heterodimerisation domain of RBP7 (RpoE)	8031874	4003624	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	Nucleic acid-binding proteins	8044251	3000135	SCOP2 (2022-06-29)
D	SCOP2 Superfamily	N-terminal, heterodimerisation domain of RBP7 (RpoE)	8044252	3001137	SCOP2 (2022-06-29)
C	SCOP2 Family	RNA polymerase II subunit RBP4 (RpoF)	8031872	4002844	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	HRDC-like	8044250	3000132	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	S1_1	e1y14B1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
B	SHS2_Rpb7-N	e1y14B2	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)
D	S1_1	e1y14D1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
D	SHS2_Rpb7-N	e1y14D2	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)
A	RNA_pol_Rpb4	e1y14A1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: RNA_pol_Rpb4	ECOD (1.6)
C	RNA_pol_Rpb4	e1y14C1	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)
B	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
B	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
D	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
D	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
A	1.20.1250.40	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
C	1.20.1250.40	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	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
B, D	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
A, C	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
B, D	DNA-directed RNA polymerase II 19 kDa polypeptide	protein binding binding translation initiation factor binding RNA binding organic cyclic compound binding nucleic acid binding single-stranded RNA binding DNA binding single-stranded DNA binding	regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process regulation of cellular process catabolic process negative regulation of biological process RNA metabolic process macromolecule catabolic process nucleobase-containing compound metabolic process negative regulation of cellular process RNA catabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process mRNA catabolic process nuclear-transcribed mRNA catabolic process regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process mRNA metabolic process nucleic acid metabolic process nucleobase-containing compound catabolic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process nucleic acid catabolic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process nucleobase-containing compound biosynthetic process RNA biosynthetic process nucleic acid biosynthetic process RNA-templated transcription DNA-templated transcription initiation DNA-templated transcription transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process translational initiation protein metabolic process positive regulation of cellular process regulation of translational initiation regulation of protein metabolic process translation positive regulation of gene expression regulation of translation positive regulation of translational initiation regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality positive regulation of nucleobase-containing compound metabolic process positive regulation of mRNA metabolic process positive regulation of RNA metabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay mRNA destabilization regulation of mRNA catabolic process RNA destabilization regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process positive regulation of nuclear-transcribed mRNA poly(A) tail shortening nuclear-transcribed mRNA poly(A) tail shortening regulation of nuclear-transcribed mRNA poly(A) tail shortening	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RPB4-RPB7 complex cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle cytoplasm supramolecular complex P-body
A, C	DNA-directed RNA polymerase II 32 kDa polypeptide	protein binding binding translation initiation factor binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound 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 nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic 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 nucleic acid biosynthetic process biosynthetic process RNA-templated transcription metabolic process cellular process macromolecule metabolic process DNA-templated transcription initiation DNA-templated transcription transcription by RNA polymerase II transcription initiation at RNA polymerase II promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation regulation of cellular process positive regulation of protein metabolic process positive regulation of biological process positive regulation of translation positive regulation of macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process translational initiation protein metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process regulation of translational initiation regulation of protein metabolic process biological regulation regulation of macromolecule metabolic process translation regulation of gene expression positive regulation of gene expression regulation of translation regulation of macromolecule biosynthetic process positive regulation of translational initiation regulation of metabolic process mRNA processing mRNA metabolic process RNA processing negative regulation of biological process regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of biological quality RNA catabolic process mRNA catabolic process positive regulation of nucleobase-containing compound metabolic process negative regulation of metabolic process positive regulation of mRNA metabolic process nucleobase-containing compound catabolic process positive regulation of RNA metabolic process negative regulation of gene expression negative regulation of macromolecule biosynthetic process nucleic acid catabolic process nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay catabolic process mRNA destabilization macromolecule catabolic process regulation of mRNA catabolic process negative regulation of cellular process negative regulation of macromolecule metabolic process RNA destabilization nuclear-transcribed mRNA catabolic process regulation of catabolic process positive regulation of catabolic process regulation of mRNA stability negative regulation of biosynthetic process positive regulation of mRNA catabolic process regulation of RNA stability regulation of mRNA metabolic process	membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex membrane-bounded organelle RNA polymerase II, holoenzyme protein-containing complex intracellular anatomical structure nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle cellular anatomical structure nucleoplasm RNA polymerase II, core complex catalytic complex intracellular membrane-bounded organelle transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen RPB4-RPB7 complex cytoplasmic ribonucleoprotein granule intracellular membraneless organelle ribonucleoprotein granule membraneless organelle cytoplasm supramolecular complex P-body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR003029	S1 domain	Domain
B, D	IPR045113	RNA polymerase subunit Rpb7-like	Family
B, D	IPR005576	RNA polymerase Rpb7-like , N-terminal	Domain
B, D	IPR036898	RNA polymerase Rpb7-like, N-terminal domain superfamily	Homologous Superfamily
B, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, C	IPR005574	RNA polymerase subunit Rpb4/RPC9	Family
A, C	IPR010997	HRDC-like superfamily	Homologous Superfamily
A, C	IPR006590	RNA polymerase Rpb4/RPC9, core	Domain
A, C	IPR038324	Rpb4/RPC9 superfamily	Homologous Superfamily
A, C	IPR045222	DNA-directed RNA polymerase II subunit Rpb4-like	Family

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.