7AOF

Atomic structure of the poxvirus transcription late pre-initiation complex


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
BPF00562e7aofB2 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: PF00562ECOD (1.6)
BPF00562e7aofB6 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: PF00562ECOD (1.6)
BPF04565e7aofB1 A: a+b complex topologyX: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)H: N-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)T: N-terminal domain in beta subunit of DNA dependent RNA-polymeraseF: PF04565ECOD (1.6)
BPF12415e7aofB5 A: a+b complex topologyX: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)H: insertion domain in beta subunit of DNA dependent RNA-polymerase (From Topology)T: insertion domain in beta subunit of DNA dependent RNA-polymeraseF: PF12415ECOD (1.6)
BPF04567e7aofB4 A: a+b complex topologyX: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)H: barrel domain in beta subunit of DNA dependent RNA-polymerase (From Topology)T: barrel domain in beta subunit of DNA dependent RNA-polymeraseF: PF04567ECOD (1.6)
BPF04560e7aofB3 A: a+b complex topologyX: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)H: C-terminal domain in beta subunit of DNA dependent RNA-polymerase (From Topology)T: C-terminal domain in beta subunit of DNA dependent RNA-polymeraseF: PF04560ECOD (1.6)
BF_UNCLASSIFIEDe7aofB7 A: a+b complex topologyX: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)H: inserted a+b domain in yeast RNA polymerase beta subunit (From Topology)T: inserted a+b domain in yeast RNA polymerase beta subunitF: F_UNCLASSIFIEDECOD (1.6)
H [auth J]PF05864e7aofJ1 A: alpha arraysX: HTHH: RPB10 (From Topology)T: RPB10F: PF05864ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF00623RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)RNA polymerase Rpb1, domain 2RNA 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
PF05000RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)RNA polymerase Rpb1, domain 4RNA 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
PF04983RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)RNA polymerase Rpb1, domain 3RNA 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
PF04998RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5)RNA polymerase Rpb1, domain 5RNA 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
PF04997RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1)RNA polymerase Rpb1, domain 1RNA 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 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 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
PF04560RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7)RNA polymerase Rpb2, domain 7RNA 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
PF04565RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3)RNA polymerase Rpb2, domain 3RNA 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
PF00562RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6)RNA polymerase Rpb2, domain 6RNA 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
PF12415Poxvirus DNA dependent RNA polymerase (rpo132)Poxvirus DNA dependent RNA polymerase- Family
PF04567RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5)RNA polymerase Rpb2, domain 5RNA 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
PF03396Poxvirus DNA-directed RNA polymerase, 35 kD subunit (Pox_RNA_pol_35)Poxvirus DNA-directed RNA polymerase, 35 kD subunit- Family
D [auth E]PF05273Poxvirus RNA polymerase 22 kDa subunit (Pox_RNA_Pol_22)Poxvirus RNA polymerase 22 kDa subunit- Family
E [auth F]PF05320Poxvirus DNA-directed RNA polymerase 19 kDa subunit (Pox_RNA_Pol_19)Poxvirus DNA-directed RNA polymerase 19 kDa subunit- Family
F [auth G]PF03293Poxvirus DNA-directed RNA polymerase, 18 kD subunit (Pox_RNA_pol)Poxvirus DNA-directed RNA polymerase, 18 kD subunit- Family
G [auth I]PF03294RNA polymerase-associated transcription specificity factor, Rap94 (Pox_Rap94)RNA polymerase-associated transcription specificity factor, Rap94- Family
H [auth J]PF05864Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7) (Chordopox_RPO7)Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7)- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
DNA-directed RNA polymerase 147 kDa polypeptide
DNA-directed RNA polymerase
DNA-directed RNA polymerase 35 kDa subunit
D [auth E]DNA-directed RNA polymerase subunit
E [auth F]DNA-directed RNA polymerase 19 kDa subunit
F [auth G]DNA-directed RNA polymerase 18 kDa subunit
G [auth I]Protein H4 -
H [auth J]DNA-directed RNA polymerase 7 kDa subunit
I [auth S]DNA-directed RNA polymerase 30 kDa polypeptide

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR007066RNA polymerase Rpb1, domain 3Domain
IPR007081RNA polymerase Rpb1, domain 5Domain
IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
IPR007083RNA polymerase Rpb1, domain 4Domain
IPR000722RNA polymerase, alpha subunitDomain
IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
IPR006592RNA polymerase, N-terminalDomain
IPR007080RNA polymerase Rpb1, domain 1Domain
IPR015712DNA-directed RNA polymerase, subunit 2Family
IPR037033DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamilyHomologous Superfamily
IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
IPR007645RNA polymerase Rpb2, domain 3Domain
IPR024390RNA polymerase, 132kDa subunit, poxvirus-typeFamily
IPR007647RNA polymerase Rpb2, domain 5Domain
IPR014724RNA polymerase Rpb2, OB-foldHomologous Superfamily
IPR007641RNA polymerase Rpb2, domain 7Domain
IPR005059DNA-directed RNA polymerase, 35kDa subunit, poxviralFamily
D [auth E]IPR007937RNA polymerase, 22kDa subunit, poxviralFamily
E [auth F]IPR007984DNA-directed RNA polymerase, 19kDa subunit, poxviralFamily
E [auth F]IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
F [auth G]IPR004973DNA-directed RNA polymerase, 18kDa subunit, poxviralFamily
G [auth I]IPR004974RNA polymerase-associated transcription specificity factor Rap94Family
H [auth J]IPR008448DNA-directed RNA polymerase, 7kDa polypeptide, chordopoxviralFamily
I [auth S]IPR001222Zinc finger, TFIIS-typeDomain
I [auth S]IPR009162RNA polymerase, 30kDa subunit, chordopox-typeFamily
I [auth S]IPR024394RNA polymerase, 30kDa subunit, chordopox-type, N-terminalDomain

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
I [auth S]SEP Parent Component: SER

RESIDAA0037

PSI-MOD :  O-phospho-L-serine MOD:00046