Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
J [auth H]d1y1yh_ Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex (Saccharomyces cerevisiae ) [TaxId: 4932 ], SCOPe (2.08)
K [auth I]d1y1yi_ Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex (Saccharomyces cerevisiae ) [TaxId: 4932 ], SCOPe (2.08)
L [auth J]d1y1yj_ Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex (Saccharomyces cerevisiae ) [TaxId: 4932 ], SCOPe (2.08)
M [auth K]d1y1yk_ Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex (Saccharomyces cerevisiae ) [TaxId: 4932 ], SCOPe (2.08)
N [auth L]d1y1yl_ Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex (Saccharomyces cerevisiae ) [TaxId: 4932 ], SCOPe (2.08)
O [auth S]d1y1ys_ Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ], SCOPe (2.08)
C [auth A]d1y1ya_ Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex (Saccharomyces cerevisiae ) [TaxId: 4932 ], SCOPe (2.08)
D [auth B]d1y1yb_ Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex (Saccharomyces cerevisiae ) [TaxId: 4932 ], SCOPe (2.08)
E [auth C]d1y1yc_ Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex (Saccharomyces cerevisiae ) [TaxId: 4932 ], SCOPe (2.08)
F [auth D]d1y1yd_ Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex (Saccharomyces cerevisiae ) [TaxId: 4932 ], SCOPe (2.08)
G [auth E]d1y1ye_ Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex (Saccharomyces cerevisiae ) [TaxId: 4932 ], SCOPe (2.08)
H [auth F]d1y1yf_ Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex (Saccharomyces cerevisiae ) [TaxId: 4932 ], SCOPe (2.08)
I [auth G]d1y1yg_ Low resolution protein structures RNA polymerase RNA polymerase RNA polymerase Complete 12-subunit RNA polymerase II complex (Saccharomyces cerevisiae ) [TaxId: 4932 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
J [auth H]SCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like 8093392 3002702 SCOP2B (2022-06-29)
J [auth H]SCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like 8041967 3002702 SCOP2B (2022-06-29)
K [auth I]SCOP2B SuperfamilyZinc beta-ribbon 8042690 3001238 SCOP2B (2022-06-29)
K [auth I]SCOP2B SuperfamilyZinc beta-ribbon 8042689 3001238 SCOP2B (2022-06-29)
L [auth J]SCOP2B SuperfamilyRNA polymerase subunit RPB10 8042692 3001213 SCOP2B (2022-06-29)
M [auth K]SCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8042694 3001655 SCOP2B (2022-06-29)
N [auth L]SCOP2B SuperfamilyRNA polymerase subunits 8042695 3001823 SCOP2B (2022-06-29)
O [auth S]SCOP2B SuperfamilyElongation factor TFIIS domain 2 8036681 3001247 SCOP2B (2022-06-29)
C [auth A]SCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8042682 3001330 SCOP2B (2022-06-29)
D [auth B]SCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8042684 3001330 SCOP2B (2022-06-29)
D [auth B]SCOP2B SuperfamilyTwo-barrel nucleic acid polymerases 8042684 3001330 SCOP2B (2022-06-29)
E [auth C]SCOP2B SuperfamilyInsert subdomain of RNA polymerase alpha subunit 8042687 3001500 SCOP2B (2022-06-29)
E [auth C]SCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8042685 3001655 SCOP2B (2022-06-29)
E [auth C]SCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8042685 3001655 SCOP2B (2022-06-29)
G [auth E]SCOP2B SuperfamilyRPB5-like RNA polymerase subunit 8035939 3001722 SCOP2B (2022-06-29)
G [auth E]SCOP2B SuperfamilyEukaryotic RPB5 N-terminal domain 8044454 3000444 SCOP2B (2022-06-29)
H [auth F]SCOP2B SuperfamilyRPB6/omega subunit-like 8042688 3000189 SCOP2B (2022-06-29)
I [auth G]SCOP2B SuperfamilyNucleic acid-binding proteins 8044251 3000135 SCOP2B (2022-06-29)
I [auth G]SCOP2B SuperfamilyN-terminal, heterodimerisation domain of RBP7 (RpoE) 8044252 3001137 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
J [auth H]RNA_pol_Rpb8e1y1yH1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: RNA_pol_Rpb8ECOD (1.6)
K [auth I]RNA_POL_M_15KDe1y1yI1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: RNA_POL_M_15KDECOD (1.6)
K [auth I]TFIIS_Ce1y1yI2 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: TFIIS_CECOD (1.6)
L [auth J]RNA_pol_Ne1y1yJ1 A: alpha arraysX: HTHH: RPB10 (From Topology)T: RPB10F: RNA_pol_NECOD (1.6)
M [auth K]RNA_pol_L_2e1y1yK1 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)
N [auth L]DNA_RNApol_7kDe1y1yL1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: DNA_RNApol_7kDECOD (1.6)
O [auth S]TFIIS_Me1y1yS1 A: alpha arraysX: RuvA-CH: Elongation factor TFIIS domain 2/ Kix domain of creb binding protein (From Topology)T: Elongation factor TFIIS domain 2/ Kix domain of creb binding proteinF: TFIIS_MECOD (1.6)
O [auth S]TFIIS_Ce1y1yS2 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: TFIIS_CECOD (1.6)
C [auth A]RNA_pol_Rpb1_2e1y1yA5 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: RNA_pol_Rpb1_2ECOD (1.6)
C [auth A]RNA_pol_Rpb1_2_1e1y1yA2 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)
C [auth A]RNA_pol_Rpb1_7e1y1yA8 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)
C [auth A]RNA_pol_Rpb1_7_1e1y1yA6 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)
C [auth A]RNA_pol_Rpb1_1e1y1yA4 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)
C [auth A]RNA_pol_Rpb1_5_3rde1y1yA1 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)
C [auth A]RNA_pol_Rpb1_6e1y1yA7 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)
C [auth A]RNA_pol_Rpb1_4e1y1yA3 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)
C [auth A]RNA_pol_Rpb1_3e1y1yA9 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)
D [auth B]RNA_pol_Rpb2_6_3rd_2e1y1yB2 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: RNA_pol_Rpb2_6_3rd_2ECOD (1.6)
D [auth B]RNA_pol_Rpb2_6_2nd_1e1y1yB7 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)
D [auth B]RNA_pol_Rpb2_3e1y1yB3 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)
D [auth B]RNA_pol_Rpb2_1e1y1yB4 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)
D [auth B]RNA_pol_Rpb2_45_1e1y1yB1 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)
D [auth B]RNA_pol_Rpb2_7e1y1yB5 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)
D [auth B]RNA_pol_Rpb2_4e1y1yB6 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)
E [auth C]RNA_pol_L_1e1y1yC1 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)
E [auth C]RNA_pol_A_bac_1e1y1yC2 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)
F [auth D]RNA_pol_Rpb4e1y1yD1 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: SAM domain-likeF: RNA_pol_Rpb4ECOD (1.6)
G [auth E]RNA_pol_Rpb5_Ce1y1yE1 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)
G [auth E]RNA_pol_Rpb5_Ne1y1yE2 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)
H [auth F]RNA_pol_Rpb6_1e1y1yF1 A: alpha arraysX: RPB6/omega subunit-like (From Homology)H: RPB6/omega subunit-likeT: RPB6F: RNA_pol_Rpb6_1ECOD (1.6)
I [auth G]S1_1e1y1yG1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: S1_1ECOD (1.6)
I [auth G]SHS2_Rpb7-Ne1y1yG2 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)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
J [auth H]PF03870RNA polymerase Rpb8 (RNA_pol_Rpb8)RNA polymerase Rpb8- Family
K [auth I]PF02150RNA polymerases M/15 Kd subunit (Zn_ribbon_RPB9)RNA polymerases M/15 Kd subunit- Domain
K [auth I]PF01096Transcription factor S-II (TFIIS) (Zn_ribbon_TFIIS)Transcription factor S-II (TFIIS)- Domain
L [auth J]PF01194RNA polymerases N / 8 kDa subunit (RNA_pol_N)RNA polymerases N / 8 kDa subunit- Domain
M [auth K]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
N [auth L]PF03604DNA directed RNA polymerase, 7 kDa subunit (Zn_ribbon_RPAB4)DNA directed RNA polymerase, 7 kDa subunit- Domain
O [auth S]PF01096Transcription factor S-II (TFIIS) (Zn_ribbon_TFIIS)Transcription factor S-II (TFIIS)- Domain
O [auth S]PF07500Transcription factor S-II (TFIIS), central domain (TFIIS_M)Transcription factor S-II (TFIIS), central domainTranscription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is comp ...Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and Pfam:PF01096 are required for transcription activity [1].
Domain
C [auth A]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
C [auth A]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
C [auth A]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
C [auth A]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
C [auth A]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
C [auth A]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
C [auth A]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
D [auth B]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
D [auth B]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
D [auth B]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
D [auth B]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
D [auth B]PF04563RNA polymerase beta subunit (RNA_pol_Rpb2_1)RNA polymerase beta subunit- Family
D [auth B]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
D [auth B]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
E [auth C]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
E [auth C]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
F [auth D]PF03874RNA polymerase Rpb4 (RNA_pol_Rpb4)RNA polymerase Rpb4- Family
G [auth E]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
G [auth E]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
H [auth F]PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
I [auth G]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
I [auth G]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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth T]5'-D(P*TP*AP*CP*GP*CP*CP*T)-3'---
J [auth H]DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
K [auth I]DNA-directed RNA polymerase II subunit 9
L [auth J]DNA-directed RNA polymerases I/II/III subunit 10
M [auth K]DNA-directed RNA polymerase II 13.6 kDa polypeptide
N [auth L]DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
O [auth S]Transcription elongation factor S-II
B [auth P]5'-R(P*AP*GP*GP*C)-3'---
C [auth A]DNA-directed RNA polymerase II largest subunit
D [auth B]DNA-directed RNA polymerase II 140 kDa polypeptide
E [auth C]DNA-directed RNA polymerase II 45 kDa polypeptide
F [auth D]DNA-directed RNA polymerase II 32 kDa polypeptide
G [auth E]DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
H [auth F]DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
I [auth G]DNA-directed RNA polymerase II 19 kDa polypeptide

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
J [auth H]IPR005570DNA-directed RNA polymerases I, II, and III subunit RPABC3Family
J [auth H]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
K [auth I]IPR001529DNA-directed RNA polymerase II subunit RPB9-like, zinc ribbonDomain
K [auth I]IPR012164DNA-directed RNA polymerase subunit/transcription factor SFamily
K [auth I]IPR001222Zinc finger, TFIIS-typeDomain
K [auth I]IPR034012Pol II subunit B9, C-terminal zinc ribbonDomain
K [auth I]IPR019761DNA-directed RNA polymerase M, 15kDa subunit, conserved siteConserved Site
L [auth J]IPR020789RNA polymerases, subunit N, zinc binding siteBinding Site
L [auth J]IPR000268DNA-directed RNA polymerase subunit RPABC5/Rpb10Family
L [auth J]IPR023580RNA polymerase subunit RPB10Homologous Superfamily
M [auth K]IPR009025DNA-directed RNA polymerase, RBP11-like dimerisation domainDomain
M [auth K]IPR037685RNA polymerase RBP11Family
M [auth K]IPR022905DNA-directed RNA polymerase subunit Rpo11-likeFamily
M [auth K]IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
M [auth K]IPR008193DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved siteConserved Site
N [auth L]IPR006591RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4Family
N [auth L]IPR029040RNA polymerase subunit RPABC4/transcription elongation factor Spt4Homologous Superfamily
N [auth L]IPR039747DNA-directed RNA polymerases I, II, and III subunit RPABC4Family
O [auth S]IPR006289Transcription elongation factor, TFIISFamily
O [auth S]IPR001222Zinc finger, TFIIS-typeDomain
O [auth S]IPR003618Transcription elongation factor S-II, central domainDomain
O [auth S]IPR035441TFIIS/LEDGF domain superfamilyHomologous Superfamily
O [auth S]IPR036575Transcription elongation factor S-II, central domain superfamilyHomologous Superfamily
O [auth S]IPR035100Transcription elongation factor, IIS-typeFamily
O [auth S]IPR017923Transcription factor IIS, N-terminalDomain
O [auth S]IPR003617Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-typeDomain
C [auth A]IPR007081RNA polymerase Rpb1, domain 5Domain
C [auth A]IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
C [auth A]IPR007075RNA polymerase Rpb1, domain 6Domain
C [auth A]IPR000684RNA polymerase II, heptapeptide repeat, eukaryoticRepeat
C [auth A]IPR007083RNA polymerase Rpb1, domain 4Domain
C [auth A]IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
C [auth A]IPR006592RNA polymerase, N-terminalDomain
C [auth A]IPR007066RNA polymerase Rpb1, domain 3Domain
C [auth A]IPR007073RNA polymerase Rpb1, domain 7Domain
C [auth A]IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
C [auth A]IPR038593RNA polymerase Rpb1, domain 7 superfamilyHomologous Superfamily
C [auth A]IPR000722RNA polymerase, alpha subunitDomain
C [auth A]IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
C [auth A]IPR007080RNA polymerase Rpb1, domain 1Domain
D [auth B]IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
D [auth B]IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
D [auth B]IPR007646RNA polymerase Rpb2, domain 4Domain
D [auth B]IPR007647RNA polymerase Rpb2, domain 5Domain
D [auth B]IPR014724RNA polymerase Rpb2, OB-foldHomologous Superfamily
D [auth B]IPR007642RNA polymerase Rpb2, domain 2Domain
D [auth B]IPR015712DNA-directed RNA polymerase, subunit 2Family
D [auth B]IPR037033DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamilyHomologous Superfamily
D [auth B]IPR037034RNA polymerase Rpb2, domain 2 superfamilyHomologous Superfamily
D [auth B]IPR007645RNA polymerase Rpb2, domain 3Domain
D [auth B]IPR007644RNA polymerase, beta subunit, protrusionDomain
D [auth B]IPR007641RNA polymerase Rpb2, domain 7Domain
E [auth C]IPR011262DNA-directed RNA polymerase, insert domainDomain
E [auth C]IPR011263DNA-directed RNA polymerase, RpoA/D/Rpb3-typeDomain
E [auth C]IPR050518Archaeal Rpo3/Eukaryotic RPB3 RNA Polymerase SubunitFamily
E [auth C]IPR022842DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1Family
E [auth C]IPR036643DNA-directed RNA polymerase, insert domain superfamilyHomologous Superfamily
E [auth C]IPR001514DNA-directed RNA polymerase, 30-40kDa subunit, conserved siteConserved Site
E [auth C]IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
F [auth D]IPR005574RNA polymerase subunit Rpb4/RPC9Family
F [auth D]IPR010997HRDC-like superfamilyHomologous Superfamily
F [auth D]IPR006590RNA polymerase Rpb4/RPC9, coreDomain
F [auth D]IPR038324Rpb4/RPC9 superfamilyHomologous Superfamily
F [auth D]IPR045222DNA-directed RNA polymerase II subunit Rpb4-likeFamily
G [auth E]IPR036710RNA polymerase Rpb5, N-terminal domain superfamilyHomologous Superfamily
G [auth E]IPR014381DNA-directed RNA polymerase subunit Rpo5/Rpb5Family
G [auth E]IPR035913RPB5-like RNA polymerase subunit superfamilyHomologous Superfamily
G [auth E]IPR000783RNA polymerase, subunit H/Rpb5 C-terminalDomain
G [auth E]IPR020608RNA polymerase, subunit H/Rpb5, conserved siteConserved Site
G [auth E]IPR005571RNA polymerase, Rpb5, N-terminalDomain
H [auth F]IPR028363DNA-directed RNA polymerase, subunit RPB6Family
H [auth F]IPR006111Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunitFamily
H [auth F]IPR020708DNA-directed RNA polymerase, 14-18kDa subunit, conserved siteConserved Site
H [auth F]IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
H [auth F]IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
I [auth G]IPR003029S1 domainDomain
I [auth G]IPR045113RNA polymerase subunit Rpb7-likeFamily
I [auth G]IPR005576RNA polymerase Rpb7-like , N-terminalDomain
I [auth G]IPR036898RNA polymerase Rpb7-like, N-terminal domain superfamilyHomologous Superfamily
I [auth G]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily