Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
FSCOP2B SuperfamilyRPB6/omega subunit-like 8106082 3000189 SCOP2B (2022-06-29)
RSCOP2B SuperfamilyRPB6/omega subunit-like 8106082 3000189 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8080728 3001655 SCOP2B (2022-06-29)
WSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8080728 3001655 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyRNA polymerase subunit RPB10 8105377 3001213 SCOP2B (2022-06-29)
VSCOP2 FamilyRNA polymerase subunit RPB10 8105376 4000742 SCOP2 (2022-06-29)
VSCOP2 SuperfamilyRNA polymerase subunit RPB10 8105377 3001213 SCOP2 (2022-06-29)
LSCOP2B SuperfamilyRNA polymerase subunits 8103068 3001823 SCOP2B (2022-06-29)
XSCOP2B SuperfamilyRNA polymerase subunits 8103068 3001823 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyHRDC-like 8101241 3000132 SCOP2B (2022-06-29)
PSCOP2B SuperfamilyHRDC-like 8101241 3000132 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ARNA_pol_Rpb1_2e7ozpA2 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: RNA_pol_Rpb1_2ECOD (1.6)
ARNA_pol_Rpb1_2_1e7ozpA5 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: RNA_pol_Rpb1_2_1ECOD (1.6)
ARNA_pol_Rpb1_7e7ozpA6 A: a+b two layersX: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)H: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)T: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunitF: RNA_pol_Rpb1_7ECOD (1.6)
ARNAP_II_Rpb1_Ce7ozpA8 A: a+b two layersX: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)H: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)T: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunitF: RNAP_II_Rpb1_CECOD (1.6)
ARNA_pol_Rpb1_5_3rde7ozpA7 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)
ARNA_pol_Rpb1_6e7ozpA4 A: a+b complex topologyX: helical domain in yeast RNA-polymerasesH: third helical domain in yeast RNA-polymerase II beta-prime subunit (From Topology)T: third helical domain in yeast RNA-polymerase II beta-prime subunitF: RNA_pol_Rpb1_6ECOD (1.6)
ARNA_pol_Rpb1_4e7ozpA1 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)
ARNA_pol_Rpb1_3e7ozpA3 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)
MRNA_pol_Rpb1_2e7ozpM2 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: RNA_pol_Rpb1_2ECOD (1.6)
MRNA_pol_Rpb1_2_1e7ozpM5 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: RNA_pol_Rpb1_2_1ECOD (1.6)
MRNA_pol_Rpb1_7e7ozpM6 A: a+b two layersX: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)H: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)T: permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunitF: RNA_pol_Rpb1_7ECOD (1.6)
MRNAP_II_Rpb1_Ce7ozpM8 A: a+b two layersX: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)H: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit (From Topology)T: ferredoxin-like domain in yeast RNA-polymerase beta-prime subunitF: RNAP_II_Rpb1_CECOD (1.6)
MRNA_pol_Rpb1_5_3rde7ozpM7 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)
MRNA_pol_Rpb1_6e7ozpM4 A: a+b complex topologyX: helical domain in yeast RNA-polymerasesH: third helical domain in yeast RNA-polymerase II beta-prime subunit (From Topology)T: third helical domain in yeast RNA-polymerase II beta-prime subunitF: RNA_pol_Rpb1_6ECOD (1.6)
MRNA_pol_Rpb1_4e7ozpM1 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)
MRNA_pol_Rpb1_3e7ozpM3 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_Rpb5_Ce7ozpE2 A: a+b two layersX: RPB5-like RNA polymerase subunit (From Topology)H: RPB5-like RNA polymerase subunit (From Topology)T: RPB5-like RNA polymerase subunitF: RNA_pol_Rpb5_CECOD (1.6)
ERNA_pol_Rpb5_Ne7ozpE1 A: a/b three-layered sandwichesX: Restriction endonuclease-likeH: Eukaryotic RPB5 N-terminal domain (From Topology)T: Eukaryotic RPB5 N-terminal domainF: RNA_pol_Rpb5_NECOD (1.6)
QRNA_pol_Rpb5_Ce7ozpQ2 A: a+b two layersX: RPB5-like RNA polymerase subunit (From Topology)H: RPB5-like RNA polymerase subunit (From Topology)T: RPB5-like RNA polymerase subunitF: RNA_pol_Rpb5_CECOD (1.6)
QRNA_pol_Rpb5_Ne7ozpQ1 A: a/b three-layered sandwichesX: Restriction endonuclease-likeH: Eukaryotic RPB5 N-terminal domain (From Topology)T: Eukaryotic RPB5 N-terminal domainF: RNA_pol_Rpb5_NECOD (1.6)
FRNA_pol_Rpb6_1e7ozpF1 A: alpha arraysX: RPB6/omega subunit-like (From Homology)H: RPB6/omega subunit-likeT: RPB6F: RNA_pol_Rpb6_1ECOD (1.6)
RRNA_pol_Rpb6_1e7ozpR1 A: alpha arraysX: RPB6/omega subunit-like (From Homology)H: RPB6/omega subunit-likeT: RPB6F: RNA_pol_Rpb6_1ECOD (1.6)
GS1_1e7ozpG1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: S1_1ECOD (1.6)
GSHS2_Rpb7-Ne7ozpG2 A: a+b two layersX: Dodecin subunit-likeH: Flavin-binding protein dodecin-like (From Topology)T: Flavin-binding protein dodecin-likeF: SHS2_Rpb7-NECOD (1.6)
SS1_1e7ozpS1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: S1_1ECOD (1.6)
SSHS2_Rpb7-Ne7ozpS2 A: a+b two layersX: Dodecin subunit-likeH: Flavin-binding protein dodecin-like (From Topology)T: Flavin-binding protein dodecin-likeF: SHS2_Rpb7-NECOD (1.6)
HRNA_pol_Rpb8e7ozpH1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: RNA_pol_Rpb8ECOD (1.6)
TRNA_pol_Rpb8e7ozpT1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: RNA_pol_Rpb8ECOD (1.6)
IRNA_POL_M_15KDe7ozpI2 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: RNA_POL_M_15KDECOD (1.6)
ITFIIS_Ce7ozpI1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: TFIIS_CECOD (1.6)
URNA_POL_M_15KDe7ozpU2 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: RNA_POL_M_15KDECOD (1.6)
UTFIIS_Ce7ozpU1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: TFIIS_CECOD (1.6)
KRNA_pol_L_2e7ozpK1 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: RNA_pol_L_2ECOD (1.6)
WRNA_pol_L_2e7ozpW1 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: RNA_pol_L_2ECOD (1.6)
JRNA_pol_Ne7ozpJ1 A: alpha arraysX: HTHH: RPB10 (From Topology)T: RPB10F: RNA_pol_NECOD (1.6)
VRNA_pol_Ne7ozpV1 A: alpha arraysX: HTHH: RPB10 (From Topology)T: RPB10F: RNA_pol_NECOD (1.6)
LDNA_RNApol_7kDe7ozpL1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: DNA_RNApol_7kDECOD (1.6)
XDNA_RNApol_7kDe7ozpX1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: DNA_RNApol_7kDECOD (1.6)
BRNA_pol_Rpb2_6_3rd_2e7ozpB2 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: RNA_pol_Rpb2_6_3rd_2ECOD (1.6)
BRNA_pol_Rpb2_6_2nd_1e7ozpB6 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: RNA_pol_Rpb2_6_2nd_1ECOD (1.6)
BRNA_pol_Rpb2_3e7ozpB1 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)
BRNA_pol_Rpb2_1e7ozpB4 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)
BRNA_pol_Rpb2_45_1e7ozpB3 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_45_1ECOD (1.6)
BRNA_pol_Rpb2_4e7ozpB5 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: RNA_pol_Rpb2_4ECOD (1.6)
NRNA_pol_Rpb2_6_3rd_2e7ozpN2 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: RNA_pol_Rpb2_6_3rd_2ECOD (1.6)
NRNA_pol_Rpb2_6_2nd_1e7ozpN6 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: RNA_pol_Rpb2_6_2nd_1ECOD (1.6)
NRNA_pol_Rpb2_3e7ozpN1 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)
NRNA_pol_Rpb2_1e7ozpN4 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)
NRNA_pol_Rpb2_45_1e7ozpN3 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_45_1ECOD (1.6)
NRNA_pol_Rpb2_4e7ozpN5 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: RNA_pol_Rpb2_4ECOD (1.6)
CRNA_pol_L_1e7ozpC2 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: RNA_pol_L_1ECOD (1.6)
CRNA_pol_A_bac_1e7ozpC1 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_bac_1ECOD (1.6)
ORNA_pol_L_1e7ozpO1 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: RNA_pol_L_1ECOD (1.6)
ORNA_pol_A_bac_1e7ozpO2 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_bac_1ECOD (1.6)
DRNA_pol_Rpb4e7ozpD1 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: SAM domain-likeF: RNA_pol_Rpb4ECOD (1.6)
PRNA_pol_Rpb4e7ozpP1 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: SAM domain-likeF: RNA_pol_Rpb4ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
E, Q
PF01191RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C)RNA polymerase Rpb5, C-terminal domainThe assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain.Domain
E, Q
PF03871RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N)RNA polymerase Rpb5, N-terminal domainRpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA p ...Rpb5 has a bipartite structure which includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H [1,2]. The N-terminal domain is involved in DNA binding and is part of the jaw module in the RNA pol II structure [3]. This module is important for positioning the downstream DNA.
Domain
F, R
PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
H, T
PF03870RNA polymerase Rpb8 (RNA_pol_Rpb8)RNA polymerase Rpb8- Family
I, U
PF02150RNA polymerases M/15 Kd subunit (Zn_ribbon_RPB9)RNA polymerases M/15 Kd subunit- Domain
I, U
PF01096Transcription factor S-II (TFIIS) (Zn_ribbon_TFIIS)Transcription factor S-II (TFIIS)- Domain
K, W
PF13656RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2)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 ...The 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 domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp. Many of the members of this family carry only the N-terminal region of Rpb11.
Domain
J, V
PF01194RNA polymerases N / 8 kDa subunit (RNA_pol_N)RNA polymerases N / 8 kDa subunit- Domain
L, X
PF03604DNA directed RNA polymerase, 7 kDa subunit (Zn_ribbon_RPAB4)DNA directed RNA polymerase, 7 kDa subunit- Domain
B, N
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 ...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 forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain [1]. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble [1]. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Domain
B, N
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
B, N
PF04566RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4)RNA polymerase Rpb2, 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). Domain 4, 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 4, is also known as the external 2 domain [1].
Domain
B, N
PF04563RNA polymerase beta subunit (RNA_pol_Rpb2_1)RNA polymerase beta subunit- Family
B, N
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
B, N
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
C, O
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 ...The 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 domain of the alpha subunit/Rpb3 is interrupted by an insert domain (Pfam:PF01000). Some of the alpha subunits also contain iron-sulphur binding domains (Pfam:PF00037). Rpb11 is found as a continuous domain. Members of this family include: alpha subunit from eubacteria, alpha subunits from chloroplasts, Rpb3 subunits from eukaryotes, Rpb11 subunits from eukaryotes, RpoD subunits from archaeal spp, and RpoL subunits from archaeal spp.
Domain
C, O
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 archaealDomain
D, P
PF03874RNA polymerase Rpb4 (RNA_pol_Rpb4)RNA polymerase Rpb4- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, M
DNA-directed RNA polymerase subunit---
E, Q
DNA-directed RNA polymerase II subunit E
F, R
DNA-directed RNA polymerase II subunit F
G, S
DNA-directed RNA polymerase II subunit RPB7---
H, T
DNA-directed RNA polymerases I, II, and III subunit RPABC3
I, U
DNA-directed RNA polymerase II subunit RPB9
K, W
RNA_pol_L_2 domain-containing protein -
J, V
DNA-directed RNA polymerases I, II, and III subunit RPABC5
L, X
RNA polymerase II subunit K
B, N
DNA-directed RNA polymerase subunit beta -
C, O
DNA-directed RNA polymerase II subunit RPB3
D, P
RNA polymerase II subunit D

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
E, Q
IPR014381DNA-directed RNA polymerase subunit Rpo5/Rpb5Family
E, Q
IPR036710RNA polymerase Rpb5, N-terminal domain superfamilyHomologous Superfamily
E, Q
IPR035913RPB5-like RNA polymerase subunit superfamilyHomologous Superfamily
E, Q
IPR000783RNA polymerase, subunit H/Rpb5 C-terminalDomain
E, Q
IPR020608RNA polymerase, subunit H/Rpb5, conserved siteConserved Site
E, Q
IPR005571RNA polymerase, Rpb5, N-terminalDomain
F, R
IPR020708DNA-directed RNA polymerase, 14-18kDa subunit, conserved siteConserved Site
F, R
IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
F, R
IPR028363DNA-directed RNA polymerase, subunit RPB6Family
F, R
IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
F, R
IPR006111Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunitFamily
H, T
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
H, T
IPR005570DNA-directed RNA polymerases I, II, and III subunit RPABC3Family
I, U
IPR001529DNA-directed RNA polymerase II subunit RPB9-like, zinc ribbonDomain
I, U
IPR012164DNA-directed RNA polymerase subunit/transcription factor SFamily
I, U
IPR001222Zinc finger, TFIIS-typeDomain
I, U
IPR034012Pol II subunit B9, C-terminal zinc ribbonDomain
I, U
IPR019761DNA-directed RNA polymerase M, 15kDa subunit, conserved siteConserved Site
K, W
IPR022905DNA-directed RNA polymerase subunit Rpo11-likeFamily
K, W
IPR009025DNA-directed RNA polymerase, RBP11-like dimerisation domainDomain
K, W
IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
K, W
IPR008193DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved siteConserved Site
K, W
IPR037685RNA polymerase RBP11Family
J, V
IPR023580RNA polymerase subunit RPB10Homologous Superfamily
J, V
IPR020789RNA polymerases, subunit N, zinc binding siteBinding Site
J, V
IPR000268DNA-directed RNA polymerase subunit RPABC5/Rpb10Family
L, X
IPR006591RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4Family
L, X
IPR029040RNA polymerase subunit RPABC4/transcription elongation factor Spt4Homologous Superfamily
L, X
IPR039747DNA-directed RNA polymerases I, II, and III subunit RPABC4Family
B, N
IPR007642RNA polymerase Rpb2, domain 2Domain
B, N
IPR015712DNA-directed RNA polymerase, subunit 2Family
B, N
IPR037033DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamilyHomologous Superfamily
B, N
IPR037034RNA polymerase Rpb2, domain 2 superfamilyHomologous Superfamily
B, N
IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
B, N
IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
B, N
IPR007645RNA polymerase Rpb2, domain 3Domain
B, N
IPR007646RNA polymerase Rpb2, domain 4Domain
B, N
IPR007647RNA polymerase Rpb2, domain 5Domain
B, N
IPR014724RNA polymerase Rpb2, OB-foldHomologous Superfamily
B, N
IPR007644RNA polymerase, beta subunit, protrusionDomain
B, N
IPR007641RNA polymerase Rpb2, domain 7Domain
C, O
IPR011262DNA-directed RNA polymerase, insert domainDomain
C, O
IPR011263DNA-directed RNA polymerase, RpoA/D/Rpb3-typeDomain
C, O
IPR050518Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase SubunitFamily
C, O
IPR022842DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1Family
C, O
IPR036643DNA-directed RNA polymerase, insert domain superfamilyHomologous Superfamily
C, O
IPR001514DNA-directed RNA polymerase, 30-40kDa subunit, conserved siteConserved Site
C, O
IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
D, P
IPR005574RNA polymerase subunit Rpb4/RPC9Family
D, P
IPR010997HRDC-like superfamilyHomologous Superfamily
D, P
IPR006590RNA polymerase Rpb4/RPC9, coreDomain
D, P
IPR038324Rpb4/RPC9 superfamilyHomologous Superfamily
D, P
IPR045222DNA-directed RNA polymerase II subunit Rpb4-likeFamily