8P0J

Cryo EM map and model of the vaccinia RNA polymerase intermediate pre-initiation open promoter complex

External Resource: Annotation

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

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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
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
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
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
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
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
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
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
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	PF12415	Poxvirus DNA dependent RNA polymerase (rpo132)	Poxvirus DNA dependent RNA polymerase	-	Family
C	PF03396	Poxvirus DNA-directed RNA polymerase, 35 kD subunit (Pox_RNA_pol_35)	Poxvirus DNA-directed RNA polymerase, 35 kD subunit	-	Family
D [auth E]	PF05273	Poxvirus RNA polymerase 22 kDa subunit (Pox_RNA_Pol_22)	Poxvirus RNA polymerase 22 kDa subunit	-	Family
G [auth H]	PF05718	Poxvirus intermediate transcription factor (Pox_int_trans)	Poxvirus intermediate transcription factor	-	Family
I [auth L]	PF03341	Poxvirus mRNA capping enzyme, small subunit (Pox_mRNA-cap)	Poxvirus mRNA capping enzyme, small subunit	-	Family
K [auth O]	PF21004	mRNA capping enzyme catalytic subunit, GTase, NTPase domain (MCEL_GT_NTPase)	mRNA capping enzyme catalytic subunit, GTase, NTPase domain	mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the meth ...	mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap [1-3]. It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module, and a C-terminal guanine-N7-methyltransferase (MTase) module (Pfam:PF03291) [4]. The N-terminal module comprises a TPase domain (Pfam:PF10640), followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase, this entry) and OB fold (Pfam:PF21005) domains [3,4]. The TPase and GTase modules stabilize their active conformations and their contacts also clamp the NTase and OB fold.	Domain
K [auth O]	PF03291	mRNA (guanine-N(7))-methyltransferase domain (mRNA_G-N7_MeTrfase)	mRNA (guanine-N(7))-methyltransferase domain	This entry represents mRNA (guanine-N(7))-methyltransferase, which can either be found as a single domain protein, or as a domain within the mRNA-capping enzyme catalytic subunit. mRNA (guanine-N(7))-methyltransferase methylates the N7 position of th ...	This entry represents mRNA (guanine-N(7))-methyltransferase, which can either be found as a single domain protein, or as a domain within the mRNA-capping enzyme catalytic subunit. mRNA (guanine-N(7))-methyltransferase methylates the N7 position of the added guanosine to the 5'-cap structure of mRNAs. It binds RNA containing 5'-terminal GpppC [1-5]. Viral mRNA capping enzymes, meanwhile, are multidomain proteins that catalyse the first two reactions in the mRNA cap formation pathway [5]. They are heterodimers consisting of a large (catalytic) and small subunit.	Domain
K [auth O]	PF10640	mRNA capping enzyme catalytic subunit, RNA triphosphatase domain (MCEL_TPase)	mRNA capping enzyme catalytic subunit, RNA triphosphatase domain	mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the meth ...	mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap [1-3]. It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module, and a C-terminal guanine-N7-methyltransferase (MTase) module (Pfam:PF03291) [4]. The N-terminal module comprises a TPase domain, represented in this entry, followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase, Pfam:PF21004) and OB fold (Pfam:PF21005) domains [4]. This domain catalyses the hydrolysis of the the 5' triphosphate end of the pre-mRNA.	Domain
K [auth O]	PF21005	mRNA-capping enzyme catalytic subunit, GTase, OB fold (MCEL_GT_OB)	mRNA-capping enzyme catalytic subunit, GTase, OB fold	mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the meth ...	mRNA-capping enzyme catalytic subunit from Vaccinia virus (MCEL, also known as mRNA-capping enzyme D1 subunit) catalyses the hydrolysis of the 5' triphosphate end of the pre-mRNA, the capping of the resulting diphosphate RNA end with GMP and the methylation of the GpppN cap [1-3]. It consists of an N-terminal RNA triphosphatase (TPase)-guanylyltransferase (GTase) module and a C-terminal guanine-N7-methyltransferase (MTase) module (Pfam:PF03291). The N-terminal module comprises a TPase domain (Pfam:PF10640), followed by the GTase at the C-terminal, which consists of the nucleotidyltransferase (NTPase, Pfam:PF21004) and OB fold (represented in this entry) domains [1]. This domain contains an essential motif (RxxK) for GTase activity.	Domain
N [auth I]	PF04745	VITF-3 subunit protein (Pox_A8)	VITF-3 subunit protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	DNA-directed RNA polymerase 147 kDa polypeptide	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
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
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
D [auth E]	DNA-directed RNA polymerase 22 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 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
F [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
G [auth H]	Intermediate transcription factor 3 large subunit	-	-	-
H [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
I [auth L]	mRNA-capping enzyme regulatory subunit OPG124	RNA methyltransferase activity catalytic activity, acting on RNA transferase activity, transferring one-carbon groups catalytic activity, acting on a nucleic acid transferase activity S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity catalytic activity mRNA methyltransferase 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	virion component
J [auth N]	Non-template DNA oligomer	-	-	-
K [auth O]	mRNA-capping enzyme catalytic subunit	guanylyltransferase activity mRNA guanylyltransferase activity RNA guanylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid transferase activity catalytic activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds polynucleotide 5'-phosphatase activity phosphatase activity hydrolase activity guanylyltransferase activity mRNA guanylyltransferase activity RNA guanylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid transferase activity catalytic activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups phosphoric ester hydrolase activity hydrolase activity, acting on ester bonds polynucleotide 5'-phosphatase activity phosphatase activity hydrolase activity pyrophosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides inorganic triphosphate phosphatase activity RNA methyltransferase activity transferase activity, transferring one-carbon groups S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity mRNA methyltransferase activity RNA binding binding nucleic acid binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding mRNA 5'-triphosphate monophosphatase activity cation binding metal ion binding	-	virion component
L [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	-	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
M [auth T]	Template DNA oligomer	-	-	-
N [auth I]	Intermediate transcription factor 3 small subunit	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007066	RNA polymerase Rpb1, domain 3	Domain
A	IPR007081	RNA polymerase Rpb1, domain 5	Domain
A	IPR045867	DNA-directed RNA polymerase, subunit beta-prime	Family
A	IPR007083	RNA polymerase Rpb1, domain 4	Domain
A	IPR000722	RNA polymerase, alpha subunit	Domain
A	IPR044893	RNA polymerase Rpb1, clamp domain superfamily	Homologous Superfamily
A	IPR038120	RNA polymerase Rpb1, funnel domain superfamily	Homologous Superfamily
A	IPR006592	RNA polymerase, N-terminal	Domain
A	IPR007080	RNA polymerase Rpb1, domain 1	Domain
B	IPR015712	DNA-directed RNA polymerase, subunit 2	Family
B	IPR037033	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily	Homologous Superfamily
B	IPR007120	DNA-directed RNA polymerase, subunit 2, hybrid-binding domain	Domain
B	IPR007121	RNA polymerase, beta subunit, conserved site	Conserved Site
B	IPR007645	RNA polymerase Rpb2, domain 3	Domain
B	IPR024390	RNA polymerase, 132kDa subunit, poxvirus-type	Family
B	IPR007647	RNA polymerase Rpb2, domain 5	Domain
B	IPR014724	RNA polymerase Rpb2, OB-fold	Homologous Superfamily
B	IPR007641	RNA polymerase Rpb2, domain 7	Domain
C	IPR005059	DNA-directed RNA polymerase, 35kDa subunit, poxviral	Family
D [auth E]	IPR007937	RNA polymerase, 22kDa subunit, poxviral	Family
E [auth F]	IPR007984	DNA-directed RNA polymerase, 19kDa subunit, poxviral	Family
E [auth F]	IPR036161	RPB6/omega subunit-like superfamily	Homologous Superfamily
F [auth G]	IPR004973	DNA-directed RNA polymerase, 18kDa subunit, poxviral	Family
G [auth H]	IPR008789	Poxvirus intermediate transcription factor	Family
H [auth J]	IPR008448	DNA-directed RNA polymerase, 7kDa polypeptide, chordopoxviral	Family
I [auth L]	IPR005009	Poxvirus mRNA capping enzyme, small subunit	Family
I [auth L]	IPR043096	Poxvirus mRNA capping enzyme, small subunit superfamily	Homologous Superfamily
K [auth O]	IPR048425	mRNA capping enzyme catalytic subunit, GTase, NTPase domain	Domain
K [auth O]	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
K [auth O]	IPR019602	mRNA capping enzyme catalytic subunit, RNA triphosphatase domain, virus	Domain
K [auth O]	IPR046430	mRNA-capping enzyme catalytic subunit, RNA triphosphatase domain superfamily	Homologous Superfamily
K [auth O]	IPR046428	mRNA-capping enzyme catalytic subunit, OB fold domain superfamily	Homologous Superfamily
K [auth O]	IPR039753	mRNA cap guanine-N7 methyltransferase	Family
K [auth O]	IPR048426	mRNA-capping enzyme catalytic subunit, GTase, OB fold	Domain
K [auth O]	IPR046429	mRNA-capping enzyme catalytic subunit, nucleotidyltransferase domain superfamily	Homologous Superfamily
K [auth O]	IPR004971	mRNA (guanine-N(7))-methyltransferase domain	Domain
L [auth S]	IPR001222	Zinc finger, TFIIS-type	Domain
L [auth S]	IPR009162	RNA polymerase, 30kDa subunit, chordopox-type	Family
L [auth S]	IPR024394	RNA polymerase, 30kDa subunit, chordopox-type, N-terminal	Domain
N [auth I]	IPR006834	VITF-3 subunit protein	Family