Annotations: 1DZF

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1dzfa1	Alpha and beta proteins (a/b)	Restriction endonuclease-like	Eukaryotic RPB5 N-terminal domain	Eukaryotic RPB5 N-terminal domain	Eukaryotic RPB5 N-terminal domain	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d1dzfa2	Alpha and beta proteins (a+b)	RPB5-like RNA polymerase subunit	RPB5-like RNA polymerase subunit	RPB5	Eukaryotic RPB5 C-terminal domain	BAKER'S YEAST (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	RPB5	8023559	4001502	SCOP2 (2022-06-29)
A	SCOP2 Family	Eukaryotic RPB5 N-terminal domain	8032076	4000501	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RPB5-like RNA polymerase subunit	8035939	3001722	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Eukaryotic RPB5 N-terminal domain	8044454	3000444	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)
A	RNA_pol_Rpb5_C	e1dzfA1	A: a+b two layers	X: RPB5-like RNA polymerase subunit (From Topology)	H: RPB5-like RNA polymerase subunit (From Topology)	T: RPB5-like RNA polymerase subunit	F: RNA_pol_Rpb5_C	ECOD (1.6)
A	RNA_pol_Rpb5_N	e1dzfA2	A: a/b three-layered sandwiches	X: Restriction endonuclease-like	H: Eukaryotic RPB5 N-terminal domain (From Topology)	T: Eukaryotic RPB5 N-terminal domain	F: RNA_pol_Rpb5_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1340.10	Alpha Beta	3-Layer(aba) Sandwich	Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide	Chain: A	CATH (4.3.0)
A	3.90.940.20	Alpha Beta	Alpha-Beta Complex	Eukaryotic RPB6 RNA polymerase subunit	RPB5-like RNA polymerase subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01191	RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C)	RNA polymerase Rpb5, C-terminal domain	The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.	Domain
A	PF03871	RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N)	RNA polymerase Rpb5, N-terminal domain	Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA p ...	Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure [3]. This module is important for positioning the downstream DNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1	DNA binding binding organic cyclic compound binding nucleic acid binding 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 component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis cellular biosynthetic process cellular 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 cellular component biogenesis ribosome biogenesis ribonucleoprotein complex biogenesis cellular process cellular component organization or biogenesis cellular biosynthetic process cellular 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 DNA-templated transcription organic cyclic compound metabolic process nucleic acid biosynthetic process transcription by RNA polymerase II organic substance metabolic process biosynthetic process organic cyclic compound biosynthetic process organic substance biosynthetic process metabolic process macromolecule metabolic process transcription by RNA polymerase III tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III ncRNA metabolic process transcription by RNA polymerase I rRNA transcription rRNA metabolic process nucleolar large rRNA transcription by RNA polymerase I DNA-templated transcription termination termination of RNA polymerase I transcription RNA-templated transcription termination of RNA polymerase III transcription transcription initiation at RNA polymerase II promoter DNA-templated transcription initiation transcription initiation at RNA polymerase III promoter transcription elongation by RNA polymerase II DNA-templated transcription elongation transcription elongation by RNA polymerase I transcription initiation at RNA polymerase I promoter	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 RNA polymerase II, holoenzyme nucleoplasm RNA polymerase II, core complex RNA polymerase III complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036710	RNA polymerase Rpb5, N-terminal domain superfamily	Homologous Superfamily
A	IPR014381	DNA-directed RNA polymerase subunit Rpo5/Rpb5	Family
A	IPR035913	RPB5-like RNA polymerase subunit superfamily	Homologous Superfamily
A	IPR000783	RNA polymerase, subunit H/Rpb5 C-terminal	Domain
A	IPR020608	RNA polymerase, subunit H/Rpb5, conserved site	Conserved Site
A	IPR005571	RNA polymerase, Rpb5, N-terminal	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.