Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8035907 3001655 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyInsert subdomain of RNA polymerase alpha subunit 8037279 3001500 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8035907 3001655 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyInsert subdomain of RNA polymerase alpha subunit 8037279 3001500 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ARNA_pol_Le6pmiA1 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: RNA_pol_LECOD (1.6)
ARNA_pol_A_bace6pmiA2 A: a+b complex topologyX: Ribosomal protein TL5/L25 C-terminal domain-likeH: Insert subdomain of RNA polymerase alpha subunit (From Topology)T: Insert subdomain of RNA polymerase alpha subunitF: RNA_pol_A_bacECOD (1.6)
BRNA_pol_Le6pmiB2 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: RNA_pol_LECOD (1.6)
BRNA_pol_A_bace6pmiB1 A: a+b complex topologyX: Ribosomal protein TL5/L25 C-terminal domain-likeH: Insert subdomain of RNA polymerase alpha subunit (From Topology)T: Insert subdomain of RNA polymerase alpha subunitF: RNA_pol_A_bacECOD (1.6)
CRNA_pol_Rpb2_6_3rde6pmiC7 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: RNA_pol_Rpb2_6_3rdECOD (1.6)
CPRK09603e6pmiC10 A: a+b two layersX: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymeraseF: PRK09603ECOD (1.6)
CRNA_pol_Rpb2_6_2nde6pmiC1 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: RNA_pol_Rpb2_6_2ndECOD (1.6)
CRNA_pol_Rpb2_6_1ste6pmiC3 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: RNA_pol_Rpb2_6_1stECOD (1.6)
CRNA_pol_Rpb2_6_2nd_2e6pmiC2 A: a+b complex topologyX: Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit (From Topology)H: Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunit (From Topology)T: Helical hairpin insertion in E. coli DNA-directed RNA polymerase beta subunitF: RNA_pol_Rpb2_6_2nd_2ECOD (1.6)
CRNA_pol_Rpb2_3e6pmiC9 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: RNA_pol_Rpb2_3ECOD (1.6)
CRNA_pol_Rpb2_1e6pmiC4 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: RNA_pol_Rpb2_1ECOD (1.6)
CRNA_pol_Rpb2_45e6pmiC6 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: RNA_pol_Rpb2_45ECOD (1.6)
CRNA_pol_Rpb2_7e6pmiC5 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: RNA_pol_Rpb2_7ECOD (1.6)
DRNA_pol_Rpb1_2e6pmiD4 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: RNA_pol_Rpb1_2ECOD (1.6)
DPRK00566_2nde6pmiD7 A: a+b two layersX: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)H: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase (From Topology)T: MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymeraseF: PRK00566_2ndECOD (1.6)
DPRK14844e6pmiD9 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: PRK14844ECOD (1.6)
DRNA_pol_Rpb1_5_1ste6pmiD5 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: RNA_pol_Rpb1_5_1stECOD (1.6)
DPRK00566_3rd,RNA_pol_Rpb1_5_3rde6pmiD3 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: PRK00566_3rd,RNA_pol_Rpb1_5_3rdECOD (1.6)
DRNA_pol_Rpb1_1e6pmiD8 A: a+b complex topologyX: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)H: N-terminal domain in RNA-polymerase beta-prime subunit (From Topology)T: N-terminal domain in RNA-polymerase beta-prime subunitF: RNA_pol_Rpb1_1ECOD (1.6)
DRNA_pol_Rpb1_5_3rde6pmiD2 A: a+b complex topologyX: central helical domain in RNA-polymerase beta-prime subunit (From Topology)H: central helical domain in RNA-polymerase beta-prime subunit (From Topology)T: central helical domain in RNA-polymerase beta-prime subunitF: RNA_pol_Rpb1_5_3rdECOD (1.6)
DRNA_pol_Rpb1_4e6pmiD6 A: a+b complex topologyX: second helical domain in RNA-polymerase beta-prime subunit (From Topology)H: second helical domain in RNA-polymerase beta-prime subunit (From Topology)T: second helical domain in RNA-polymerase beta-prime subunitF: RNA_pol_Rpb1_4ECOD (1.6)
DRNA_pol_Rpb1_3e6pmiD1 A: a+b complex topologyX: first helical domain in RNA-polymerase beta-prime subunit (From Topology)H: first helical domain in RNA-polymerase beta-prime subunit (From Topology)T: first helical domain in RNA-polymerase beta-prime subunitF: RNA_pol_Rpb1_3ECOD (1.6)
ERNA_pol_Rpb6e6pmiE1 A: alpha arraysX: RPB6/omega subunit-like (From Homology)H: RPB6/omega subunit-likeT: RNA polymerase omega subunitF: RNA_pol_Rpb6ECOD (1.6)
FSigma70_r3e6pmiF3 A: alpha arraysX: HTHH: HTHT: tri-helicalF: Sigma70_r3ECOD (1.6)
FSigma70_r4_2e6pmiF1 A: alpha arraysX: HTHH: HTHT: tri-helicalF: Sigma70_r4_2ECOD (1.6)
FSigma70_r2_2e6pmiF2 A: alpha complex topologyX: Sigma2 domain-likeH: Sigma2 domain of RNA polymerase sigma factors (From Topology)T: Sigma2 domain of RNA polymerase sigma factorsF: Sigma70_r2_2ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B
PF01193RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L)RNA polymerase Rpb3/Rpb11 dimerisation domainThe two eukaryotic subunits Rpb3 and Rpb11 dimerise to from a platform onto which the other subunits of the RNA polymerase assemble (D/L in archaea). The prokaryotic equivalent of the Rpb3/Rpb11 platform is the alpha-alpha dimer. The dimerisation do ...Domain
A, B
PF01000RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac)RNA polymerase Rpb3/RpoA insert domainMembers of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal Domain
PF04561RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2)RNA polymerase Rpb2, 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). Rpb2 is the second largest subunit of the RNA po ...Domain
PF10385RNA polymerase beta subunit external 1 domain (RNA_pol_Rpb2_45)RNA polymerase beta subunit external 1 domainRNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between ...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 ...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 ...Domain
PF04563RNA polymerase beta subunit (RNA_pol_Rpb2_1)RNA polymerase beta subunit- Family
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 ...Domain
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 ...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 ...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 ...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 ...Domain
PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
PF04539Sigma-70 region 3 (Sigma70_r3)Sigma-70 region 3- Family
PF04542Sigma-70 region 2 (Sigma70_r2)Sigma-70 region 2Region 2 of sigma-70 is the most conserved region of the entire protein. All members of this class of sigma-factor contain region 2. The high conservation is due to region 2 containing both the -10 promoter recognition helix and the primary core RNA ...Domain
PF04545Sigma-70, region 4 (Sigma70_r4)Sigma-70, region 4Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [1]. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix fami ...Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B
DNA-directed RNA polymerase subunit alpha
DNA-directed RNA polymerase subunit beta
DNA-directed RNA polymerase subunit beta'
DNA-directed RNA polymerase subunit omega
RNA polymerase sigma factor FliA
G [auth 1]SYNTHETIC NONTEMPLATE STRAND DNA (54-MER)---
H [auth 2]SYNTHETIC TEMPLATE STRAND DNA (54-MER)---
I [auth 3]Nascent RNA---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B
IPR011773DNA-directed RNA polymerase, alpha subunitFamily
A, B
IPR011260RNA polymerase, alpha subunit, C-terminalDomain
A, B
IPR011263DNA-directed RNA polymerase, RpoA/D/Rpb3-typeDomain
A, B
IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
A, B
IPR011262DNA-directed RNA polymerase, insert domainDomain
A, B
IPR036643DNA-directed RNA polymerase, insert domain superfamilyHomologous Superfamily
IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
IPR014724RNA polymerase Rpb2, OB-foldHomologous Superfamily
IPR007642RNA polymerase Rpb2, domain 2Domain
IPR015712DNA-directed RNA polymerase, subunit 2Family
IPR037033DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamilyHomologous Superfamily
IPR042107DNA-directed RNA polymerase, beta subunit, external 1 domain superfamilyHomologous Superfamily
IPR037034RNA polymerase Rpb2, domain 2 superfamilyHomologous Superfamily
IPR007645RNA polymerase Rpb2, domain 3Domain
IPR019462DNA-directed RNA polymerase, beta subunit, external 1 domainDomain
IPR010243DNA-directed RNA polymerase beta subunit, bacterial-typeFamily
IPR007644RNA polymerase, beta subunit, protrusionDomain
IPR007641RNA polymerase Rpb2, domain 7Domain
IPR007081RNA polymerase Rpb1, domain 5Domain
IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
IPR007083RNA polymerase Rpb1, domain 4Domain
IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
IPR006592RNA polymerase, N-terminalDomain
IPR007066RNA polymerase Rpb1, domain 3Domain
IPR012754DNA-directed RNA polymerase, subunit beta-prime, bacterial typeFamily
IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
IPR000722RNA polymerase, alpha subunitDomain
IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
IPR007080RNA polymerase Rpb1, domain 1Domain
IPR003716DNA-directed RNA polymerase, omega subunitFamily
IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
IPR007627RNA polymerase sigma-70 region 2Domain
IPR000943RNA polymerase sigma-70Domain
IPR012845RNA polymerase sigma factor, FliA/WhiGFamily
IPR013325RNA polymerase sigma factor, region 2Homologous Superfamily
IPR013324RNA polymerase sigma factor, region 3/4-likeHomologous Superfamily
IPR007630RNA polymerase sigma-70 region 4Domain
IPR014284RNA polymerase sigma-70-like domainDomain
IPR007624RNA polymerase sigma-70 region 3Domain
IPR028617RNA polymerase sigma factor FliAFamily