2RF4

Crystal structure of the RNA Polymerase I subcomplex A14/43

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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	d2rf4b_	Small proteins	RNA polymerase I subunit A14-like	RNA polymerase I subunit A14-like	RNA polymerase I subunit A14	RNA polymerase I subunit A14	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
D	d2rf4d_	Small proteins	RNA polymerase I subunit A14-like	RNA polymerase I subunit A14-like	RNA polymerase I subunit A14	RNA polymerase I subunit A14	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
F	d2rf4f_	Small proteins	RNA polymerase I subunit A14-like	RNA polymerase I subunit A14-like	RNA polymerase I subunit A14	RNA polymerase I subunit A14	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2rf4a2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	RNA polymerase I subunit A43, C-terminal domain	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2rf4a1	Alpha and beta proteins (a+b)	Dodecin subunit-like	N-terminal, heterodimerisation domain of RBP7 (RpoE)	RNA polymerase I subunit A43, N-terminal domain	RNA polymerase I subunit A43, N-terminal domain	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d2rf4c2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	RNA polymerase I subunit A43, C-terminal domain	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d2rf4c1	Alpha and beta proteins (a+b)	Dodecin subunit-like	N-terminal, heterodimerisation domain of RBP7 (RpoE)	RNA polymerase I subunit A43, N-terminal domain	RNA polymerase I subunit A43, N-terminal domain	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d2rf4e2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	RNA polymerase I subunit A43, C-terminal domain	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
E	d2rf4e1	Alpha and beta proteins (a+b)	Dodecin subunit-like	N-terminal, heterodimerisation domain of RBP7 (RpoE)	RNA polymerase I subunit A43, N-terminal domain	RNA polymerase I subunit A43, N-terminal domain	Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ], Baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	PF08203	e2rf4B1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF08203	ECOD (1.6)
D	PF08203	e2rf4D1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF08203	ECOD (1.6)
F	PF08203	e2rf4F1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: PF08203	ECOD (1.6)
A	PF17875	e2rf4A6	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF17875	ECOD (1.6)
A	PF03876	e2rf4A5	A: a+b two layers	X: Dodecin subunit-like	H: Flavin-binding protein dodecin-like (From Topology)	T: Flavin-binding protein dodecin-like	F: PF03876	ECOD (1.6)
C	PF17875	e2rf4C6	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF17875	ECOD (1.6)
C	PF03876	e2rf4C5	A: a+b two layers	X: Dodecin subunit-like	H: Flavin-binding protein dodecin-like (From Topology)	T: Flavin-binding protein dodecin-like	F: PF03876	ECOD (1.6)
E	PF17875	e2rf4E6	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: PF17875	ECOD (1.6)
E	PF03876	e2rf4E5	A: a+b two layers	X: Dodecin subunit-like	H: Flavin-binding protein dodecin-like (From Topology)	T: Flavin-binding protein dodecin-like	F: PF03876	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	6.10.250.3390	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
D	6.10.250.3390	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
F	6.10.250.3390	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
A	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
C	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
C	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
E	3.30.1490.120	Alpha Beta	2-Layer Sandwich	Dna Ligase	domain 1	CATH (4.3.0)
E	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F	PF08203	Yeast RNA polymerase I subunit RPA14 (RNA_polI_A14)	Yeast RNA polymerase I subunit RPA14	-	Family
A, C, E	PF17875	RPA43 OB domain in RNA Pol I (RPA43_OB)	RPA43 OB domain in RNA Pol I	This is OB domain found in RPA43 proteins (DNA-directed RNA polymerase I subunit RPA43, also known as A43) in yeast. Functional analysis of RNA polymerase I show that, subunits A14 and A43 form the heterodimer A14/43, which is distantly related to Rp ...	This is OB domain found in RPA43 proteins (DNA-directed RNA polymerase I subunit RPA43, also known as A43) in yeast. Functional analysis of RNA polymerase I show that, subunits A14 and A43 form the heterodimer A14/43, which is distantly related to Rpb4/7 in Pol II and C17/25 in Pol III [1]. Crystal structure analysis show that A43-A14 heterodimer forms the stalk that provides a platform for initiation factors and interacts with newly synthesized RNA [3].	Domain
A, C, E	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D, F	DNA-directed RNA polymerase I subunit RPA4	DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity RNA polymerase I 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 RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I rRNA transcription organic substance biosynthetic process rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I cellular metabolic process primary metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I rRNA transcription organic substance biosynthetic process rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process ncRNA metabolic process metabolic process cellular process macromolecule metabolic process DNA-templated transcription termination termination of RNA polymerase I transcription transcription elongation by RNA polymerase I DNA-templated transcription elongation cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis transcription initiation at RNA polymerase I promoter DNA-templated transcription initiation cellular component organization regulation of cellular component size biological regulation regulation of biological quality regulation of cell size regulation of anatomical structure size	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle intracellular non-membrane-bounded organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen
A, C, E	DNA-directed RNA polymerase I subunit RPA4	DNA-directed 5'-3' RNA polymerase activity 5'-3' RNA polymerase activity RNA polymerase I 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 RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I rRNA transcription organic substance biosynthetic process rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I cellular metabolic process primary metabolic process cellular biosynthetic process RNA metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process organic substance metabolic process transcription by RNA polymerase I rRNA transcription organic substance biosynthetic process rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I cellular metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process ncRNA metabolic process metabolic process cellular process macromolecule metabolic process DNA-templated transcription termination termination of RNA polymerase I transcription cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular component organization or biogenesis transcription elongation by RNA polymerase I DNA-templated transcription elongation transcription initiation at RNA polymerase I promoter DNA-templated transcription initiation	membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity membrane-bounded organelle protein-containing complex intracellular anatomical structure RNA polymerase I complex nucleus membrane-enclosed lumen nuclear protein-containing complex transferase complex intracellular organelle lumen intracellular organelle non-membrane-bounded organelle catalytic complex intracellular membrane-bounded organelle cellular anatomical entity nucleolus transferase complex, transferring phosphorus-containing groups nuclear DNA-directed RNA polymerase complex organelle lumen organelle intracellular non-membrane-bounded organelle RNA polymerase complex DNA-directed RNA polymerase complex intracellular protein-containing complex nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F	IPR013239	RNA polymerase I, subunit Rpa14, fungi	Family
A, C, E	IPR045113	RNA polymerase subunit Rpb7-like	Family
A, C, E	IPR005576	RNA polymerase Rpb7-like , N-terminal	Domain
A, C, E	IPR036898	RNA polymerase Rpb7-like, N-terminal domain superfamily	Homologous Superfamily
A, C, E	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, C, E	IPR041178	RPA43, OB domain	Domain
A, C, E	IPR041901	Rpa43, N-terminal ribonucleoprotein (RNP) domain	Domain

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.