8XMD

Pre-translocated Pol IV transcription elongation complex


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
JSCOP2B SuperfamilyRNA polymerase subunit RPB10 8106328 3001213 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyRNA polymerase subunits 8106336 3001823 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRPB6/omega subunit-like 8106334 3000189 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF00623RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2)RNA polymerase Rpb1, domain 2RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 2, contains the active site. The invariant motif -NADFDGD- binds the active site magnesium ion [1,2].
Domain
PF05000RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4)RNA polymerase Rpb1, domain 4RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel do ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 4, represents the funnel domain. The funnel contain the binding site for some elongation factors [1,2].
Domain
PF04983RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3)RNA polymerase Rpb1, domain 3RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore doma ...RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [1,2].
Domain
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
PF05183RNA dependent RNA polymerase (RdRP)RNA dependent RNA polymerase- 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
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
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 IV subunit 1
DNA-directed RNA polymerases II, IV and V subunit 10
DNA-directed RNA polymerases II, IV and V subunit 11
DNA-directed RNA polymerases II, IV and V subunit 12
RNA-dependent RNA polymerase 2
Nontemplate_DNA---
RNA---
P [auth Q]Template_DNA---
DNA-directed RNA polymerases IV and V subunit 2
DNA-directed RNA polymerases II, IV and V subunit 3
DNA-directed RNA polymerases IV and V subunit 4
DNA-directed RNA polymerases II and IV subunit 5A
DNA-directed RNA polymerases II, IV and V subunit 6A
DNA-directed RNA polymerase IV subunit 7-
DNA-directed RNA polymerases II, IV and V subunit 8B
DNA-directed RNA polymerases II, IV and V subunit 9A

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR007066RNA polymerase Rpb1, domain 3Domain
IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
IPR040402DNA-directed RNA polymerase IV/V subunit 1, C-terminalDomain
IPR007083RNA polymerase Rpb1, domain 4Domain
IPR040403DNA-directed RNA polymerase IV/V subunit 1, N-terminalDomain
IPR000722RNA polymerase, alpha subunitDomain
IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
IPR006592RNA polymerase, N-terminalDomain
IPR023580RNA polymerase subunit RPB10Homologous Superfamily
IPR020789RNA polymerases, subunit N, zinc binding siteBinding Site
IPR000268DNA-directed RNA polymerase subunit RPABC5/Rpb10Family
IPR022905DNA-directed RNA polymerase subunit Rpo11-likeFamily
IPR009025DNA-directed RNA polymerase, RBP11-like dimerisation domainDomain
IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
IPR008193DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved siteConserved Site
IPR037685RNA polymerase RBP11Family
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
IPR007855RNA-dependent RNA polymerase, eukaryotic-typeFamily
IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
IPR007646RNA polymerase Rpb2, domain 4Domain
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
IPR014381DNA-directed RNA polymerase subunit Rpo5/Rpb5Family
IPR035913RPB5-like RNA polymerase subunit superfamilyHomologous Superfamily
IPR036710RNA polymerase Rpb5, N-terminal domain superfamilyHomologous Superfamily
IPR000783RNA polymerase, subunit H/Rpb5 C-terminalDomain
IPR020608RNA polymerase, subunit H/Rpb5, conserved siteConserved Site
IPR005571RNA polymerase, Rpb5, N-terminalDomain
IPR020708DNA-directed RNA polymerase, 14-18kDa subunit, conserved siteConserved Site
IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
IPR028363DNA-directed RNA polymerase, subunit RPB6Family
IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
IPR006111Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunitFamily
IPR036898RNA polymerase Rpb7-like, N-terminal domain superfamilyHomologous Superfamily
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR045113RNA polymerase subunit Rpb7-likeFamily
IPR005576RNA polymerase Rpb7-like , N-terminalDomain
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR005570DNA-directed RNA polymerases I, II, and III subunit RPABC3Family
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