2CKZ | pdb_00002ckz

X-ray structure of RNA polymerase III subcomplex C17-C25.

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	HMG_CoA_synt_N	e2ckzD2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: HMG_CoA_synt_N	ECOD (v294.1)
D	DUF4982	e2ckzD3	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: DUF4982	ECOD (v294.1)
B	PHP	e2ckzB3	A: a/b three-layered sandwiches	X: Fusion glycoprotein F2	H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase	F: PHP	ECOD (v294.1)
B	DUF4982	e2ckzB2	A: a/b three-layered sandwiches	X: DP domain	H: DP domain	T: DP domain	F: DUF4982	ECOD (v294.1)
C	TFIIS_M	e2ckzC1	A: a/b three-layered sandwiches	X: RuvA-C	H: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	T: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein	F: TFIIS_M	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
C	1.20.1250.40	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
A	6.10.140.870	Special	Helix non-globular	Helix Hairpins		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	PF08292	RNA polymerase III subunit Rpc25 (RNA_pol_Rbc25)	RNA polymerase III subunit Rpc25	Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating ...	Rpc25 is a strongly conserved subunit of RNA polymerase III and has homology to Rpa43 in RNA polymerase I, Rpb7 in RNA polymerase II and the archaeal RpoE subunit. Rpc25 is required for transcription initiation and is not essential for the elongating properties of RNA polymerase III [1].	Domain
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
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 III 25 KD POLYPEPTIDE	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	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription termination nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process termination of RNA polymerase III transcription biosynthetic process metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription termination nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process termination of RNA polymerase III transcription biosynthetic process metabolic process cellular process macromolecule metabolic process transcription by RNA polymerase III DNA-templated transcription initiation transcription initiation at RNA polymerase III promoter tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III	membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure organelle RNA polymerase complex RNA polymerase III complex membrane-bounded organelle protein-containing complex intracellular anatomical structure catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle cellular anatomical structure organelle RNA polymerase complex RNA polymerase III complex DNA-directed RNA polymerase complex intracellular protein-containing complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen
A, C	DNA-DIRECTED RNA POLYMERASE III 18 KD POLYPEPTIDE	binding nucleoside phosphate 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 DNA-templated transcription termination nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process termination of RNA polymerase III transcription biosynthetic process metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process DNA-templated transcription termination nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process termination of RNA polymerase III transcription biosynthetic process metabolic process cellular process macromolecule metabolic process transcription by RNA polymerase III DNA-templated transcription initiation transcription initiation at RNA polymerase III promoter tRNA metabolic process tRNA transcription tRNA transcription by RNA polymerase III	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex catalytic complex nucleus nuclear protein-containing complex intracellular membrane-bounded organelle transferase complex transferase complex, transferring phosphorus-containing groups intracellular organelle organelle RNA polymerase complex RNA polymerase III complex DNA-directed RNA polymerase complex intracellular protein-containing complex membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR045113	RNA polymerase subunit Rpb7-like	Family
B, D	IPR005576	RNA polymerase Rpb7-like , N-terminal	Domain
B, D	IPR013238	RNA polymerase III, subunit Rpc25	Domain
B, D	IPR036898	RNA polymerase Rpb7-like, N-terminal domain superfamily	Homologous Superfamily
B, D	IPR004519	DNA-directed RNA polymerase, subunit E/RPC8	Family
B, D	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
A, C	IPR005574	RNA polymerase subunit Rpb4/RPC9	Family
A, C	IPR038846	DNA-directed RNA polymerase III subunit RPC9	Family
A, C	IPR010997	HRDC-like superfamily	Homologous Superfamily
A, C	IPR038324	Rpb4/RPC9 superfamily	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.