8C8H

Cryo EM structure of the vaccinia complete RNA polymerase complex lacking the capping enzyme

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B]	PF04560	RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)	RNA polymerase Rpb2, domain 7	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA p ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Rpb2 is the second largest subunit of the RNA polymerase. This domain comprised of the structural domains anchor and clamp [1]. The clamp region (C-terminal) contains a zinc-binding motif [1]. The clamp region is named due to its interaction with the clamp domain found in Rpb1. The domain also contains a region termed "switch 4". The switches within the polymerase are thought to signal different stages of transcription [1].	Domain
A [auth B]	PF04565	RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)	RNA polymerase Rpb2, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 3, s also known as the fork domain and is proximal to catalytic site [1].	Domain
A [auth B]	PF00562	RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)	RNA polymerase Rpb2, domain 6	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain represents the hybrid binding domain and the wall domain [1]. The hybrid binding domain binds the nascent RNA strand / template DNA strand in the Pol II transcription elongation complex. This domain contains the important structural motifs, switch 3 and the flap loop and binds an active site metal ion[1]. This domain is also involved in binding to Rpb1 and Rpb3 [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 2 (DRII).	Domain
A [auth B]	PF12415	Poxvirus DNA dependent RNA polymerase (rpo132)	Poxvirus DNA dependent RNA polymerase	-	Family
A [auth B]	PF04567	RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5)	RNA polymerase Rpb2, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain [1].	Domain
B [auth E]	PF05273	Poxvirus RNA polymerase 22 kDa subunit (Pox_RNA_Pol_22)	Poxvirus RNA polymerase 22 kDa subunit	-	Family
G [auth R], K [auth Q]	PF06138	Chordopoxvirus E11 protein (Chordopox_E11)	Chordopoxvirus E11 protein	-	Family
J [auth A]	PF00623	RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)	RNA polymerase Rpb1, domain 2	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].	Domain
J [auth A]	PF05000	RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)	RNA polymerase Rpb1, domain 4	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].	Domain
J [auth A]	PF04983	RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)	RNA polymerase Rpb1, domain 3	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].	Domain
J [auth A]	PF04998	RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)	RNA polymerase Rpb1, domain 5	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontin ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 5, represents the discontinuous cleft domain that is required to from the central cleft or channel where the DNA is bound [1,2].	Domain
J [auth A]	PF04997	RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)	RNA polymerase Rpb1, domain 1	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp dom ...	RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [1,2].	Domain
L [auth Y]	PF00271	Helicase conserved C-terminal domain (Helicase_C)	Helicase conserved C-terminal domain	The Prosite family is restricted to DEAD/H helicases, whereas this domain family is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase.	Domain
L [auth Y]	PF00176	SNF2-related domain (SNF2-rel_dom)	SNF2-related domain	This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as w ...	This domain is found in proteins involved in a variety of processes including transcription regulation (e.g., SNF2, STH1, brahma, MOT1), DNA repair (e.g., ERCC6, RAD16, RAD5), DNA recombination (e.g., RAD54), and chromatin unwinding (e.g., ISWI) as well as a variety of other proteins with little functional information (e.g., lodestar, ETL1)[1,2,3]. SNF2 functions as the ATPase component of the SNF2/SWI multisubunit complex, which utilises energy derived from ATP hydrolysis to disrupt histone-DNA interactions, resulting in the increased accessibility of DNA to transcription factors.	Domain
L [auth Y]	PF08469	Nucleoside triphosphatase I C-terminal (NPHI_C)	Nucleoside triphosphatase I C-terminal	-	Family
M [auth C]	PF03396	Poxvirus DNA-directed RNA polymerase, 35 kD subunit (Pox_RNA_pol_35)	Poxvirus DNA-directed RNA polymerase, 35 kD subunit	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth B]	DNA-directed RNA polymerase 133 kDa polypeptide	DNA binding binding nucleic acid binding ribonucleoside binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding small molecule binding cation binding ion binding metal ion binding	-	virion component 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 E]	DNA-directed RNA polymerase 22 kDa subunit	DNA binding binding nucleic acid binding	viral gene expression DNA-templated viral transcription viral process viral transcription	virion component 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
C [auth F]	DNA-directed RNA polymerase 19 kDa subunit	DNA binding binding nucleic acid binding	-	virion component 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
D [auth G]	DNA-directed RNA polymerase 18 kDa subunit	DNA binding binding nucleic acid binding	viral gene expression viral process viral transcription	virion component 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
E [auth I]	RNA polymerase-associated transcription-specificity factor RAP94	transcription regulator activity DNA-binding transcription factor activity	RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression DNA-templated transcription termination macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression DNA-templated transcription termination macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process viral gene expression DNA-templated viral transcription viral process viral transcription	virion component
F [auth J]	DNA-directed RNA polymerase 7 kDa subunit	DNA binding binding nucleic acid binding	-	virion component 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
G [auth R], K [auth Q]	Core protein E11	-	-	virion component
H [auth K]	Early transcription factor 82 kDa subunit	DNA binding binding nucleic acid binding	regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of cellular process positive regulation of DNA-templated transcription positive regulation of biological process RNA metabolic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process positive regulation of metabolic process DNA-templated transcription regulation of RNA metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process positive regulation of nucleobase-containing compound metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process cellular process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process	virion component
I [auth U]	chr17.trna16-GlnTTG	-	-	-
J [auth A]	DNA-directed RNA polymerase 147 kDa polypeptide	DNA binding binding nucleic acid binding	viral gene expression DNA-templated viral transcription viral process viral transcription	virion component 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
L [auth Y]	Nucleoside triphosphatase I	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding pyrophosphatase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	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 nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	virion component
M [auth C]	DNA-directed RNA polymerase 35 kDa subunit	DNA binding binding nucleic acid binding	viral gene expression viral process viral transcription	virion component 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
N [auth S]	DNA-directed RNA polymerase 30 kDa polypeptide	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	viral gene expression DNA-templated viral transcription viral process viral transcription	virion component host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region 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 B]	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
A [auth B]	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
A [auth B]	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
A [auth B]	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
A [auth B]	IPR007645	RNA polymerase Rpb2, domain 3	Domain
A [auth B]	IPR024390	RNA polymerase, 132kDa subunit, poxvirus-type	Family
A [auth B]	IPR007647	RNA polymerase Rpb2, domain 5	Domain
A [auth B]	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
A [auth B]	IPR007641	RNA polymerase Rpb2, domain 7	Domain
B [auth E]	IPR007937	RNA polymerase, 22kDa subunit, poxviral	Family
C [auth F]	IPR007984	DNA-directed RNA polymerase, 19kDa subunit, poxviral	Family
C [auth F]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
D [auth G]	IPR004973	DNA-directed RNA polymerase, 18kDa subunit, poxviral	Family
E [auth I]	IPR004974	RNA polymerase-associated transcription specificity factor Rap94	Family
F [auth J]	IPR008448	DNA-directed RNA polymerase, 7kDa polypeptide, chordopoxviral	Family
G [auth R], K [auth Q]	IPR009201	Virion core protein, vaccinia E11L type	Family
H [auth K]	IPR007532	Poxvirus early transcription factor, large subunit	Family
J [auth A]	IPR007066	RNA polymerase Rpb1, domain 3	Domain
J [auth A]	IPR007081	RNA polymerase Rpb1, domain 5	Domain
J [auth A]	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
J [auth A]	IPR007083	RNA polymerase Rpb1, domain 4	Domain
J [auth A]	IPR000722	RNA polymerase, alpha subunit	Domain
J [auth A]	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
J [auth A]	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
J [auth A]	IPR006592	RNA polymerase, N-terminal	Domain
J [auth A]	IPR007080	RNA polymerase Rpb1, domain 1	Domain
L [auth Y]	IPR000330	SNF2, N-terminal	Domain
L [auth Y]	IPR013676	Nucleoside triphosphatase I, C-terminal	Domain
L [auth Y]	IPR001650	Helicase, C-terminal domain-like	Domain
L [auth Y]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
L [auth Y]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
M [auth C]	IPR005059	DNA-directed RNA polymerase, 35kDa subunit, poxviral	Family
N [auth S]	IPR001222	Zinc finger, TFIIS-type	Domain
N [auth S]	IPR009162	RNA polymerase, 30kDa subunit, chordopox-type	Family
N [auth S]	IPR024394	RNA polymerase, 30kDa subunit, chordopox-type, N-terminal	Domain