4V1N

Architecture of the RNA polymerase II-Mediator core transcription initiation complex


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ASCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8042682 3001330 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyRNA polymerase subunit RPB10 8042692 3001213 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8042694 3001655 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyRNA polymerase subunits 8042695 3001823 SCOP2B (2022-06-29)
MSCOP2B SuperfamilyZinc beta-ribbon 8082617 3001238 SCOP2B (2022-06-29)
OSCOP2B SuperfamilyTATA-box binding protein-like 8036831 3000705 SCOP2B (2022-06-29)
OSCOP2B SuperfamilyTATA-box binding protein-like 8036833 3000705 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8042684 3001330 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8042684 3001330 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyInsert subdomain of RNA polymerase alpha subunit 8042687 3001500 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8042685 3001655 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8042685 3001655 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyEukaryotic RPB5 N-terminal domain 8044454 3000444 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyRPB5-like RNA polymerase subunit 8035939 3001722 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRPB6/omega subunit-like 8042688 3000189 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyN-terminal, heterodimerisation domain of RBP7 (RpoE) 8044252 3001137 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyNucleic acid-binding proteins 8044251 3000135 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like 8041967 3002702 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like 8093392 3002702 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyZinc beta-ribbon 8042689 3001238 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyZinc beta-ribbon 8042690 3001238 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
ARNA_pol_Rpb1_2e4v1nA4 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: RNA_pol_Rpb1_2ECOD (1.6)
ARNA_pol_Rpb1_2_1e4v1nA5 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_7e4v1nA6 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)
ARNA_pol_Rpb1_7_1e4v1nA1 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: RNA_pol_Rpb1_7_1ECOD (1.6)
ARNA_pol_Rpb1_1e4v1nA2 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)
ARNA_pol_Rpb1_5_3rde4v1nA3 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_6e4v1nA9 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_4e4v1nA7 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_3e4v1nA8 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)
JRNA_pol_Ne4v1nJ1 A: alpha arraysX: HTHH: RPB10 (From Topology)T: RPB10F: RNA_pol_NECOD (1.6)
KRNA_pol_L_2e4v1nK1 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)
LDNA_RNApol_7kDe4v1nL1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: DNA_RNApol_7kDECOD (1.6)
MTFIIBe4v1nM1 A: alpha arraysX: HTHH: HTHT: Cyclin-likeF: TFIIBECOD (1.6)
MTF_Zn_Ribbone4v1nM3 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: TF_Zn_RibbonECOD (1.6)
OTBPe4v1nO1 A: a+b two layersX: TBP-likeH: TATA-box binding protein-like (From Topology)T: TATA-box binding protein-likeF: TBPECOD (1.6)
QTFIIF_alpha_Ne4v1nQ1 A: beta complex topologyX: triple barrel (From Homology)H: triple barrelT: Rap30/74 interaction domains-likeF: TFIIF_alpha_NECOD (1.6)
RTFIIF_beta_Ne4v1nR1 A: beta complex topologyX: triple barrel (From Homology)H: triple barrelT: Rap30/74 interaction domains-likeF: TFIIF_beta_NECOD (1.6)
BRNA_pol_Rpb2_6_3rd_2e4v1nB6 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: RNA_pol_Rpb2_6_3rd_2ECOD (1.6)
BRNA_pol_Rpb2_6_2nd_1e4v1nB7 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_3e4v1nB2 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_1e4v1nB5 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_1e4v1nB1 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_7e4v1nB3 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)
BRNA_pol_Rpb2_4e4v1nB4 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_1e4v1nC2 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_1e4v1nC1 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_Rpb4e4v1nD1 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: SAM domain-likeF: RNA_pol_Rpb4ECOD (1.6)
ERNA_pol_Rpb5_Ce4v1nE1 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_Ne4v1nE2 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_1e4v1nF1 A: alpha arraysX: RPB6/omega subunit-like (From Homology)H: RPB6/omega subunit-likeT: RPB6F: RNA_pol_Rpb6_1ECOD (1.6)
GS1_1e4v1nG2 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: S1_1ECOD (1.6)
GSHS2_Rpb7-Ne4v1nG1 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_Rpb8e4v1nH1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: RNA_pol_Rpb8ECOD (1.6)
IRNA_POL_M_15KDe4v1nI2 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: RNA_POL_M_15KDECOD (1.6)
ITFIIS_Ce4v1nI1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: TFIIS_CECOD (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
PF04990RNA polymerase Rpb1, domain 7 (RNA_pol_Rpb1_7)RNA polymerase Rpb1, 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). This domain, domain 7, represents a mobile modu ...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 7, represents a mobile module of the RNA polymerase. Domain 7 forms a substantial interaction with the lobe domain of Rpb2 (Pfam:PF04561) [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
PF04992RNA polymerase Rpb1, domain 6 (RNA_pol_Rpb1_6)RNA polymerase Rpb1, 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, domain 6, represents a mobile modu ...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 6, represents a mobile module of the RNA polymerase. Domain 6 forms part of the shelf module [1,2]. This family appears to be specific to the largest subunit of RNA polymerase II.
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
PF01194RNA polymerases N / 8 kDa subunit (RNA_pol_N)RNA polymerases N / 8 kDa subunit- Domain
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
PF03604DNA directed RNA polymerase, 7 kDa subunit (DNA_RNApol_7kD)DNA directed RNA polymerase, 7 kDa subunit- Domain
PF00382Transcription factor TFIIB repeat (TFIIB)Transcription factor TFIIB repeat- Domain
PF08271TFIIB zinc-binding (TF_Zn_Ribbon)TFIIB zinc-bindingThe transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ...The transcription factor TFIIB contains a zinc-binding motif near the N-terminus. This domain is involved in the interaction with RNA pol II and TFIIF and plays a crucial role in selecting the transcription initiation site. The domain adopts a zinc ribbon like structure [1].
Domain
PF00352Transcription factor TFIID (or TATA-binding protein, TBP) (TBP)Transcription factor TFIID (or TATA-binding protein, TBP)- Domain
PF17683TFIIF, beta subunit N-terminus (TFIIF_beta_N)TFIIF, beta subunit N-terminus- Family
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
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
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
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 ...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
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
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
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
PF03874RNA polymerase Rpb4 (RNA_pol_Rpb4)RNA polymerase Rpb4- Family
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
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
PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
PF03876SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N)SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ...Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3].
Domain
PF00575S1 RNA binding domain (S1)S1 RNA binding domainThe S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.Domain
PF03870RNA polymerase Rpb8 (RNA_pol_Rpb8)RNA polymerase Rpb8- Family
PF02150RNA polymerases M/15 Kd subunit (RNA_POL_M_15KD)RNA polymerases M/15 Kd subunit- Domain
PF01096Transcription factor S-II (TFIIS) (TFIIS_C)Transcription factor S-II (TFIIS)- Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
TRANSCRIPTION INITIATION FACTOR IIB
NONTEMPLATE DNA---
TATA-BOX-BINDING PROTEIN
RNA---
TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT ALPHA
TRANSCRIPTION INITIATION FACTOR IIF SUBUNIT BETA
S [auth T]TEMPLATE DNA---
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR007081RNA polymerase Rpb1, domain 5Domain
IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
IPR007075RNA polymerase Rpb1, domain 6Domain
IPR000684RNA polymerase II, heptapeptide repeat, eukaryoticRepeat
IPR007083RNA polymerase Rpb1, domain 4Domain
IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
IPR006592RNA polymerase, N-terminalDomain
IPR007066RNA polymerase Rpb1, domain 3Domain
IPR007073RNA polymerase Rpb1, domain 7Domain
IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
IPR038593RNA polymerase Rpb1, domain 7 superfamilyHomologous Superfamily
IPR000722RNA polymerase, alpha subunitDomain
IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
IPR007080RNA polymerase Rpb1, domain 1Domain
IPR020789RNA polymerases, subunit N, zinc binding siteBinding Site
IPR000268DNA-directed RNA polymerase subunit RPABC5/Rpb10Family
IPR023580RNA polymerase subunit RPB10Homologous Superfamily
IPR009025DNA-directed RNA polymerase, RBP11-like dimerisation domainDomain
IPR037685RNA polymerase RBP11Family
IPR022905DNA-directed RNA polymerase subunit Rpo11-likeFamily
IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
IPR008193DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved siteConserved Site
IPR006591RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4Family
IPR029040RNA polymerase subunit RPABC4/transcription elongation factor Spt4Homologous Superfamily
IPR039747DNA-directed RNA polymerases I, II, and III subunit RPABC4Family
IPR000812Transcription factor TFIIBFamily
IPR023486Transcription factor TFIIB, conserved siteConserved Site
IPR013150Transcription factor TFIIB, cyclin-like domainDomain
IPR013137Zinc finger, TFIIB-typeDomain
IPR036915Cyclin-like superfamilyHomologous Superfamily
IPR013763Cyclin-like domainDomain
IPR030491TATA-box binding protein, conserved siteConserved Site
IPR000814TATA-box binding proteinFamily
IPR012295TBP domain superfamilyHomologous Superfamily
IPR033710TATA-box binding protein, eukaryoticFamily
IPR008851Transcription initiation factor IIF, alpha subunitFamily
IPR011039Transcription Factor IIF, Rap30/Rap74, interactionHomologous Superfamily
IPR003196Transcription initiation factor IIF, beta subunitFamily
IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
IPR040450TFIIF beta subunit, HTH domainDomain
IPR040504TFIIF, beta subunit, N-terminalDomain
IPR011039Transcription Factor IIF, Rap30/Rap74, interactionHomologous Superfamily
IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
IPR007646RNA polymerase Rpb2, domain 4Domain
IPR007647RNA polymerase Rpb2, domain 5Domain
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
IPR037034RNA polymerase Rpb2, domain 2 superfamilyHomologous Superfamily
IPR007645RNA polymerase Rpb2, domain 3Domain
IPR007644RNA polymerase, beta subunit, protrusionDomain
IPR007641RNA polymerase Rpb2, domain 7Domain
IPR011262DNA-directed RNA polymerase, insert domainDomain
IPR011263DNA-directed RNA polymerase, RpoA/D/Rpb3-typeDomain
IPR050518Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase SubunitFamily
IPR022842DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1Family
IPR036643DNA-directed RNA polymerase, insert domain superfamilyHomologous Superfamily
IPR001514DNA-directed RNA polymerase, 30-40kDa subunit, conserved siteConserved Site
IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
IPR005574RNA polymerase subunit Rpb4/RPC9Family
IPR010997HRDC-like superfamilyHomologous Superfamily
IPR006590RNA polymerase Rpb4/RPC9, coreDomain
IPR038324Rpb4/RPC9 superfamilyHomologous Superfamily
IPR045222DNA-directed RNA polymerase II subunit Rpb4-likeFamily
IPR036710RNA polymerase Rpb5, N-terminal domain superfamilyHomologous Superfamily
IPR014381DNA-directed RNA polymerase subunit Rpo5/Rpb5Family
IPR035913RPB5-like RNA polymerase subunit superfamilyHomologous Superfamily
IPR000783RNA polymerase, subunit H/Rpb5 C-terminalDomain
IPR020608RNA polymerase, subunit H/Rpb5, conserved siteConserved Site
IPR005571RNA polymerase, Rpb5, N-terminalDomain
IPR028363DNA-directed RNA polymerase, subunit RPB6Family
IPR006111Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunitFamily
IPR020708DNA-directed RNA polymerase, 14-18kDa subunit, conserved siteConserved Site
IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
IPR003029S1 domainDomain
IPR045113RNA polymerase subunit Rpb7-likeFamily
IPR005576RNA polymerase Rpb7-like , N-terminalDomain
IPR036898RNA polymerase Rpb7-like, N-terminal domain superfamilyHomologous Superfamily
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR005570DNA-directed RNA polymerases I, II, and III subunit RPABC3Family
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR012164DNA-directed RNA polymerase subunit/transcription factor SFamily
IPR001222Zinc finger, TFIIS-typeDomain
IPR034012Pol II subunit B9, C-terminal zinc ribbonDomain
IPR019761DNA-directed RNA polymerase M, 15kDa subunit, conserved siteConserved Site
IPR001529DNA-directed RNA polymerase, M/15kDa subunitDomain