Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ESCOP2B SuperfamilyEukaryotic RPB5 N-terminal domain8044454 3000444 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyRPB5-like RNA polymerase subunit8035939 3001722 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRPB6/omega subunit-like8042688 3000189 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyRNA polymerase subunits8042695 3001823 SCOP2B (2022-06-29)
OSCOP2B SuperfamilyMediator subcomplex-like8051777 3001613 SCOP2B (2022-06-29)
PSCOP2B SuperfamilyMediator of RNA polymerase II transcription subunit 178091516 3002517 SCOP2B (2022-06-29)
QSCOP2B SuperfamilyCYTH-like phosphatases8090011 3001426 SCOP2B (2022-06-29)
SSCOP2B SuperfamilyMediator subcomplex-like8051778 3001613 SCOP2B (2022-06-29)
BA [auth b]SCOP2B SuperfamilyTFB5-like8086592 3000733 SCOP2B (2022-06-29)
NA [auth n]SCOP2 FamilyBromodomain extra-terminal (BET) domain-like8046364 4005043 SCOP2 (2022-06-29)
NA [auth n]SCOP2 FamilyYEATS domain-like8051392 4007347 SCOP2 (2022-06-29)
NA [auth n]SCOP2 SuperfamilyBromodomain extra-terminal (BET) domain-like8053738 3002220 SCOP2 (2022-06-29)
NA [auth n]SCOP2 SuperfamilyYEATS domain-like8053741 3002221 SCOP2 (2022-06-29)
ASCOP2B SuperfamilyTwo-barrel nucleic acid polymerases8042682 3001330 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyRNA polymerase subunit RPB108042692 3001213 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase8042694 3001655 SCOP2B (2022-06-29)
NSCOP2B SuperfamilyMediator of RNA polymerase II transcription subunit 88091509 3002515 SCOP2B (2022-06-29)
RSCOP2B SuperfamilyCYTH-like phosphatases8091513 3001426 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyTwo-barrel nucleic acid polymerases8042684 3001330 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyTwo-barrel nucleic acid polymerases8042684 3001330 SCOP2B (2022-06-29)
USCOP2B SuperfamilyMediator subcomplex-like8034652 3001613 SCOP2B (2022-06-29)
WSCOP2B SuperfamilyMediator subcomplex-like8034654 3001613 SCOP2B (2022-06-29)
XSCOP2B SuperfamilyMediator of RNA polymerase II transcription subunit 318105980 3002846 SCOP2B (2022-06-29)
CA [auth c]SCOP2B SuperfamilyZinc beta-ribbon8082617 3001238 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase8042685 3001655 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyInsert subdomain of RNA polymerase alpha subunit8042687 3001500 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase8042685 3001655 SCOP2B (2022-06-29)
DA [auth d]SCOP2B SuperfamilyTranscription factor IIA (TFIIA) beta-barrel domain8036836 3001281 SCOP2B (2022-06-29)
DA [auth d]SCOP2B SuperfamilyTranscription factor IIA (TFIIA) alpha-helical domain8036834 3001887 SCOP2B (2022-06-29)
EA [auth e]SCOP2B SuperfamilyTranscription factor IIA (TFIIA) alpha-helical domain8036837 3001887 SCOP2B (2022-06-29)
JA [auth j]SCOP2B SuperfamilyTATA-box binding protein-like8036831 3000705 SCOP2B (2022-06-29)
JA [auth j]SCOP2B SuperfamilyTATA-box binding protein-like8036833 3000705 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyNucleic acid-binding proteins8044251 3000135 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyN-terminal heterodimerisation domain of RBP7 (RpoE)8044252 3001137 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like8093392 3002702 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRBP8/CHS5 N-terminal domain-like8041967 3002702 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyZinc beta-ribbon8042690 3001238 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyZinc beta-ribbon8042689 3001238 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
EPF01191e5svaE1 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: PF01191ECOD (1.6)
EPF03871e5svaE2 A: a/b three-layered sandwichesX: Restriction endonuclease-likeH: Eukaryotic RPB5 N-terminal domain (From Topology)T: Eukaryotic RPB5 N-terminal domainF: PF03871ECOD (1.6)
FPF01192e5svaF1 A: alpha arraysX: RPB6/omega subunit-like (From Homology)H: RPB6/omega subunit-likeT: RPB6F: PF01192ECOD (1.6)
LPF03604e5svaL1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF03604ECOD (1.6)
OPF10280e5svaO1 A: a+b complex topologyX: Mediator of RNA polymerase II transcription subunit 11 (From Topology)H: Mediator of RNA polymerase II transcription subunit 11 (From Topology)T: Mediator of RNA polymerase II transcription subunit 11F: PF10280ECOD (1.6)
PPF10156e5svaP1 A: a+b complex topologyX: Mediator of RNA polymerase II transcription subunit 17 (From Topology)H: Mediator of RNA polymerase II transcription subunit 17 (From Topology)T: Mediator of RNA polymerase II transcription subunit 17F: PF10156ECOD (1.6)
QPF09637e5svaQ1 A: a+b complex topologyX: mRNA triphosphatase CET1-related (From Topology)H: mRNA triphosphatase CET1-related (From Topology)T: mRNA triphosphatase CET1-relatedF: PF09637ECOD (1.6)
SPF06179e5svaS1 A: a+b complex topologyX: Mediator of RNA polymerase II transcription subunit 22 (From Topology)H: Mediator of RNA polymerase II transcription subunit 22 (From Topology)T: Mediator of RNA polymerase II transcription subunit 22F: PF06179ECOD (1.6)
AA [auth a]PF18307e5svaa1 A: a+b complex topologyX: TFB5-related (From Topology)H: TFB5-related (From Topology)T: TFB5-relatedF: PF18307ECOD (1.6)
BA [auth b]PF06331e5svab1 A: a+b complex topologyX: TFB5-related (From Topology)H: TFB5-related (From Topology)T: TFB5-relatedF: PF06331ECOD (1.6)
FA [auth f]PF05793e5svaf1 A: beta complex topologyX: triple barrel (From Homology)H: triple barrelT: Rap30/74 interaction domains-likeF: PF05793ECOD (1.6)
GA [auth g]PF17683e5svag1 A: beta complex topologyX: triple barrel (From Homology)H: triple barrelT: Rap30/74 interaction domains-likeF: PF17683ECOD (1.6)
GA [auth g]PF02270e5svag2 A: alpha arraysX: HTHH: HTHT: wingedF: PF02270ECOD (1.6)
HA [auth h]PF02002e5svah2 A: alpha arraysX: HTHH: HTHT: wingedF: PF02002ECOD (1.6)
HA [auth h]F_UNCLASSIFIEDe5svah1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: F_UNCLASSIFIEDECOD (1.6)
APF00623e5svaA9 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: PF00623ECOD (1.6)
APF00623e5svaA3 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: PF00623ECOD (1.6)
APF04990e5svaA1 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: PF04990ECOD (1.6)
AF_UNCLASSIFIEDe5svaA5 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: F_UNCLASSIFIEDECOD (1.6)
APF04997e5svaA2 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: PF04997ECOD (1.6)
APF04998e5svaA7 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: PF04998ECOD (1.6)
APF04992e5svaA6 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: PF04992ECOD (1.6)
APF04998,PF05000e5svaA8 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: PF04998,PF05000ECOD (1.6)
APF04983e5svaA4 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: PF04983ECOD (1.6)
JPF01194e5svaJ1 A: alpha arraysX: HTHH: RPB10 (From Topology)T: RPB10F: PF01194ECOD (1.6)
KPF13656e5svaK1 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: PF13656ECOD (1.6)
MPF04934e5svaM1 A: extended segmentsX: Mediator of RNA polymerase II transcription subunit 6 (From Topology)H: Mediator of RNA polymerase II transcription subunit 6 (From Topology)T: Mediator of RNA polymerase II transcription subunit 6F: PF04934ECOD (1.6)
NPF10232e5svaN1 A: a+b complex topologyX: Mediator of RNA polymerase II transcription subunit 8 (From Topology)H: Mediator of RNA polymerase II transcription subunit 8 (From Topology)T: Mediator of RNA polymerase II transcription subunit 8F: PF10232ECOD (1.6)
RPF08612e5svaR1 A: a+b complex topologyX: mRNA triphosphatase CET1-related (From Topology)H: mRNA triphosphatase CET1-related (From Topology)T: mRNA triphosphatase CET1-relatedF: PF08612ECOD (1.6)
BPF00562e5svaB4 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: double psiF: PF00562ECOD (1.6)
BPF00562e5svaB1 A: a+b complex topologyX: alpha/beta-Hammerhead/Barrel-sandwich hybridH: alpha/beta-Hammerhead/Barrel-sandwich hybridT: Single hybrid motifF: PF00562ECOD (1.6)
BPF04563,PF04565e5svaB3 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: PF04563,PF04565ECOD (1.6)
BPF04561e5svaB5 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: PF04561ECOD (1.6)
BPF00562,PF04567e5svaB2 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: PF00562,PF04567ECOD (1.6)
BPF00562,PF04560e5svaB6 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: PF00562,PF04560ECOD (1.6)
BPF04566e5svaB7 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: PF04566ECOD (1.6)
UPF05983e5svaU1 A: alpha duplicates or obligate multimersX: Mediator hinge subcomplex-like (From Homology)H: Mediator hinge subcomplex-likeT: MED7 hinge regionF: PF05983ECOD (1.6)
UPF05983e5svaU2 A: a+b complex topologyX: Mediator of RNA polymerase II transcription submodule Med7N/31 (From Topology)H: Mediator of RNA polymerase II transcription submodule Med7N/31 (From Topology)T: Mediator of RNA polymerase II transcription submodule Med7N/31F: PF05983ECOD (1.6)
WPF11221e5svaW1 A: alpha duplicates or obligate multimersX: Mediator hinge subcomplex-like (From Homology)H: Mediator hinge subcomplex-likeT: RNA polymerase II holoenzyme component SRB7 (MED21)F: PF11221ECOD (1.6)
XPF05669e5svaX1 A: a+b complex topologyX: Mediator of RNA polymerase II transcription submodule Med7N/31 (From Topology)H: Mediator of RNA polymerase II transcription submodule Med7N/31 (From Topology)T: Mediator of RNA polymerase II transcription submodule Med7N/31F: PF05669ECOD (1.6)
YPF06733e5svaY3 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: PF06733ECOD (1.6)
YPF13307e5svaY2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: PF13307ECOD (1.6)
ZPF04851e5svaZ1 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: PF04851ECOD (1.6)
ZPF16203e5svaZ2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: PF16203ECOD (1.6)
CA [auth c]PF00382e5svac1 A: alpha arraysX: HTHH: HTHT: Cyclin-likeF: PF00382ECOD (1.6)
CA [auth c]PF08271e5svac2 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF08271ECOD (1.6)
CPF01193e5svaC2 A: a+b two layersX: DCoH-likeH: RBP11-like subunits of RNA polymerase (From Topology)T: RBP11-like subunits of RNA polymeraseF: PF01193ECOD (1.6)
CPF01000e5svaC1 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: PF01000ECOD (1.6)
DA [auth d]PF03153e5svad1 A: beta duplicates or obligate multimersX: Transcription factor IIA (TFIIA), beta-barrel domain (From Topology)H: Transcription factor IIA (TFIIA), beta-barrel domain (From Topology)T: Transcription factor IIA (TFIIA), beta-barrel domainF: PF03153ECOD (1.6)
DA [auth d]PF03153e5svad2 A: alpha duplicates or obligate multimersX: TFIIA, alpha-helical domain (From Topology)H: TFIIA, alpha-helical domain (From Topology)T: TFIIA, alpha-helical domainF: PF03153ECOD (1.6)
EA [auth e]PF02751e5svae2 A: beta duplicates or obligate multimersX: Transcription factor IIA (TFIIA), beta-barrel domain (From Topology)H: Transcription factor IIA (TFIIA), beta-barrel domain (From Topology)T: Transcription factor IIA (TFIIA), beta-barrel domainF: PF02751ECOD (1.6)
EA [auth e]PF02268e5svae1 A: alpha duplicates or obligate multimersX: TFIIA, alpha-helical domain (From Topology)H: TFIIA, alpha-helical domain (From Topology)T: TFIIA, alpha-helical domainF: PF02268ECOD (1.6)
IA [auth i]PF02186e5svai2 A: alpha arraysX: HTHH: HTHT: wingedF: PF02186ECOD (1.6)
IA [auth i]PF18121e5svai1 A: alpha arraysX: HTHH: HTHT: wingedF: PF18121ECOD (1.6)
JA [auth j]PF00352e5svaj2 A: a+b two layersX: TBP-likeH: TATA-box binding protein-like (From Topology)T: TATA-box binding protein-likeF: PF00352ECOD (1.6)
DPF03874e5svaD1 A: alpha arraysX: HhH/H2THH: SAM/DNA-glycosylaseT: SAM domain-likeF: PF03874ECOD (1.6)
GPF00575e5svaG1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF00575ECOD (1.6)
GPF03876e5svaG2 A: a+b two layersX: Dodecin subunit-likeH: Flavin-binding protein dodecin-like (From Topology)T: Flavin-binding protein dodecin-likeF: PF03876ECOD (1.6)
HPF03870e5svaH1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF03870ECOD (1.6)
IPF01096e5svaI1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF01096ECOD (1.6)
IPF02150e5svaI2 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: PF02150ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
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
PF03604DNA directed RNA polymerase, 7 kDa subunit (DNA_RNApol_7kD)DNA directed RNA polymerase, 7 kDa subunit- Domain
PF10280Mediator complex protein (Med11)Mediator complex protein- Family
PF10156Subunit 17 of Mediator complex (Med17)Subunit 17 of Mediator complex- Family
PF09637Med18 protein (Med18)Med18 proteinMed18 is one subunit of Mediator, a head-module multiprotein complex, that stimulates basal RNA polymerase II (Pol II) transcription. Med18 consists of an eight-stranded beta-barrel with a central pore and three flanking helices. It complexes with Me ...Med18 is one subunit of Mediator, a head-module multiprotein complex, that stimulates basal RNA polymerase II (Pol II) transcription. Med18 consists of an eight-stranded beta-barrel with a central pore and three flanking helices. It complexes with Med8 and Med20 proteins by forming a heterodimer of two-fold symmetry with Med20 and binding the C-terminal alpha-helix region of Med8 across the top of its barrel. This complex creates a multipartite TBP-binding site that can be modulated by transcriptional activators [1].
Domain
PF06179Surfeit locus protein 5 subunit 22 of Mediator complex (Med22)Surfeit locus protein 5 subunit 22 of Mediator complex- Family
PF10018Vitamin-D-receptor interacting Mediator subunit 4 (Med4)Vitamin-D-receptor interacting Mediator subunit 4- Family
AA [auth a]PF18307Transcription factor Tfb2 (p52) C-terminal domain (Tfb2_C)Transcription factor Tfb2 (p52) C-terminal domainThis is the C-terminal domain of Transcription factor Tfb2 present in Saccharomyces cerevisiae. Tfb2 is referred to as p52 in humans. The interaction between p8-Tfb5 and p52-Tfb2 has a key role in the maintenance of the transcription factor TFIIH arc ...This is the C-terminal domain of Transcription factor Tfb2 present in Saccharomyces cerevisiae. Tfb2 is referred to as p52 in humans. The interaction between p8-Tfb5 and p52-Tfb2 has a key role in the maintenance of the transcription factor TFIIH architecture and TFIIHs function in nucleotide-excision repair (NER) pathway. The C-terminal domain of Tfb2 is thought to have a crucial role in DNA repair [1].
Domain
BA [auth b]PF06331Transcription factor TFIIH complex subunit Tfb5 (Tfb5)Transcription factor TFIIH complex subunit Tfb5- Family
GA [auth g]PF02270TFIIF, beta subunit HTH domain (TFIIF_beta)TFIIF, beta subunit HTH domainAccurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which ...Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIF (TFIIF) is a tetramer of two beta subunits associate with two alpha subunits which interacts directly with RNA polymerase II. The beta subunit of TFIIF is required for recruitment of RNA polymerase II onto the promoter.
Domain
GA [auth g]PF17683TFIIF, beta subunit N-terminus (TFIIF_beta_N)TFIIF, beta subunit N-terminus- Family
KA [auth k]PF05001RNA polymerase Rpb1 C-terminal repeat (RNA_pol_Rpb1_R)RNA polymerase Rpb1 C-terminal repeat- Repeat
NA [auth n]PF17035Bromodomain extra-terminal - transcription regulation (BET)Bromodomain extra-terminal - transcription regulationThe BET, or bromodomain extra-terminal domain, is found on bromodomain proteins that play key roles in development, cancer progression and virus-host pathogenesis. It interacts with NSD3, JMJD6, CHD4, GLTSCR1, and ATAD5 all of which are shown to impa ...The BET, or bromodomain extra-terminal domain, is found on bromodomain proteins that play key roles in development, cancer progression and virus-host pathogenesis. It interacts with NSD3, JMJD6, CHD4, GLTSCR1, and ATAD5 all of which are shown to impart a pTEFb-independent transcriptional activation function on the bromodomain proteins [1].
Domain
NA [auth n]PF03366YEATS family (YEATS)YEATS familyWe have named this family the YEATS family, after `YNK7', `ENL', `AF-9', and `TFIIF small subunit'. This family also contains the GAS41 protein. All these proteins are thought to have a transcription stimulatory activityDomain
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
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
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
PF04934MED6 mediator sub complex component (Med6)MED6 mediator sub complex component- Family
PF10232Mediator of RNA polymerase II transcription complex subunit 8 (Med8)Mediator of RNA polymerase II transcription complex subunit 8- Family
PF08612TATA-binding related factor (TRF) of subunit 20 of Mediator complex (Med20)TATA-binding related factor (TRF) of subunit 20 of Mediator complex- 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
PF05983MED7 protein (Med7)MED7 protein- Family
PF07544RNA polymerase II transcription mediator complex subunit 9 (Med9)RNA polymerase II transcription mediator complex subunit 9- Family
PF11221Subunit 21 of Mediator complex (Med21)Subunit 21 of Mediator complex- Family
PF05669SOH1 (Med31)SOH1- Family
PF06733DEAD_2 (DEAD_2)DEAD_2- Family
PF06777Helical and beta-bridge domain (HBB)Helical and beta-bridge domainHBB is the domain on DEAD-box eukaryotic DNA repair helicases (EC:3.6.1.-) that appears to be a unique fold. It's conformation is of alpha-helices 12-16 plus a short beta-bridge to the FeS-cluster domain at the N-terminal. The full-length XPD protein ...HBB is the domain on DEAD-box eukaryotic DNA repair helicases (EC:3.6.1.-) that appears to be a unique fold. It's conformation is of alpha-helices 12-16 plus a short beta-bridge to the FeS-cluster domain at the N-terminal. The full-length XPD protein verifies the presence of damage to DNA and allows DNA repair to proceed. XPD is an assembly of several domains to form a doughnut-shaped molecule that is able to separate two DNA strands and scan the DNA for damage. HBB helps to form the overall DNA-clamping architecture [1]. This family represents a conserved region within a number of eukaryotic DNA repair helicases (EC:3.6.1.-).
Domain
PF04851Type III restriction enzyme, res subunit (ResIII)Type III restriction enzyme, res subunit- Family
CA [auth c]PF00382Transcription factor TFIIB repeat (TFIIB)Transcription factor TFIIB repeat- Domain
CA [auth c]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
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
EA [auth e]PF02751Transcription initiation factor IIA, gamma subunit (TFIIA_gamma_C)Transcription initiation factor IIA, gamma subunitAccurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA b ...Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The C-terminal domain of the gamma subunit is a 12 stranded beta-barrel.
Domain
EA [auth e]PF02268Transcription initiation factor IIA, gamma subunit, helical domain (TFIIA_gamma_N)Transcription initiation factor IIA, gamma subunit, helical domainAccurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA ...Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II. Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The N-terminal domain of the gamma subunit is a 4 helix bundle.
Domain
IA [auth i]PF18121TFA2 Winged helix domain 2 (TFA2_Winged_2)TFA2 Winged helix domain 2This is the second winged helix domain can be found in TFA2 proteins present in Saccharomyces cerevisiae. In form 2, the domain interacts directly with Rad3, a DNA helicase [1].Domain
IA [auth i]PF02186TFIIE beta subunit core domain (TFIIE_beta)TFIIE beta subunit core domainGeneral transcription factor TFIIE consists of two subunits, TFIIE alpha Pfam:PF02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymer ...General transcription factor TFIIE consists of two subunits, TFIIE alpha Pfam:PF02002 and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The structure of the DNA binding core region has been solved [1] and has a winged helix fold.
Domain
JA [auth j]PF00352Transcription factor TFIID (or TATA-binding protein, TBP) (TBP)Transcription factor TFIID (or TATA-binding protein, TBP)- Domain
PF03874RNA polymerase Rpb4 (RNA_pol_Rpb4)RNA polymerase Rpb4- 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 polymerases I, II, and III subunit RPABC1
DNA-directed RNA polymerases I, II, and III subunit RPABC2
DNA-directed RNA polymerases I, II, and III subunit RPABC4
Mediator of RNA polymerase II transcription subunit 11
Mediator of RNA polymerase II transcription subunit 17
Mediator of RNA polymerase II transcription subunit 18
Mediator of RNA polymerase II transcription subunit 22
Mediator of RNA polymerase II transcription subunit 4
AA [auth a]RNA polymerase II transcription factor B subunit 2
BA [auth b]RNA polymerase II transcription factor B subunit 5-
FA [auth f]Transcription initiation factor IIF subunit alpha
GA [auth g]Transcription initiation factor IIF subunit beta
HA [auth h]Transcription initiation factor IIE subunit alpha
KA [auth k]DNA-directed RNA polymerase II subunit RPB1
NA [auth n]Transcription initiation factor TFIID subunit 14
DNA-directed RNA polymerase II subunit RPB1
DNA-directed RNA polymerases I, II, and III subunit RPABC5
DNA-directed RNA polymerase II subunit RPB11
Mediator of RNA polymerase II transcription subunit 6
Mediator of RNA polymerase II transcription subunit 8
Mediator of RNA polymerase II transcription subunit 20
DNA-directed RNA polymerase II subunit RPB2
Mediator of RNA polymerase II transcription subunit 7
Mediator of RNA polymerase II transcription subunit 9
Mediator of RNA polymerase II transcription subunit 21
Mediator of RNA polymerase II transcription subunit 31
DNA repair helicase RAD3
DNA repair helicase RAD25
CA [auth c]Transcription initiation factor IIB
DNA-directed RNA polymerase II subunit RPB3
DA [auth d]Transcription initiation factor IIA large subunit
EA [auth e]Transcription initiation factor IIA subunit 2
IA [auth i]Transcription initiation factor IIE subunit beta
JA [auth j]TATA-box-binding protein
LA [auth l]108bp HIS4 Promoter Non-template Strand (-92/+16)---
MA [auth m]108bp HIS4 Promoter Template Strand (+16/-92)---
DNA-directed RNA polymerase II subunit RPB4
DNA-directed RNA polymerase II subunit RPB7
DNA-directed RNA polymerases I, II, and III subunit RPABC3
DNA-directed RNA polymerase II subunit RPB9

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
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
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
IPR019404Mediator complex, subunit Med11Family
IPR019313Mediator complex, subunit Med17Family
IPR019095Mediator complex, subunit Med18Family
IPR009332Mediator of RNA polymerase II transcription subunit 22Family
IPR016530Mediator of RNA polymerase II transcription subunit 22, SaccharomycetesFamily
IPR019258Mediator complex, subunit Med4Family
AA [auth a]IPR040662Transcription factor Tfb2, C-terminal domainDomain
AA [auth a]IPR004598Transcription factor TFIIH subunit p52/Tfb2Family
BA [auth b]IPR009400TFIIH subunit TTDA/Tfb5Family
BA [auth b]IPR035935TFB5-like superfamilyHomologous Superfamily
FA [auth f]IPR008851Transcription initiation factor IIF, alpha subunitFamily
FA [auth f]IPR011039Transcription Factor IIF, Rap30/Rap74, interactionHomologous Superfamily
GA [auth g]IPR003196Transcription initiation factor IIF, beta subunitFamily
GA [auth g]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
GA [auth g]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
GA [auth g]IPR040450TFIIF beta subunit, HTH domainDomain
GA [auth g]IPR040504TFIIF, beta subunit, N-terminalDomain
GA [auth g]IPR011039Transcription Factor IIF, Rap30/Rap74, interactionHomologous Superfamily
HA [auth h]IPR024550TFIIEalpha/SarR/Rpc3 HTH domainDomain
HA [auth h]IPR013083Zinc finger, RING/FYVE/PHD-typeHomologous Superfamily
HA [auth h]IPR039997Transcription factor EFamily
HA [auth h]IPR017919Transcription factor TFE/TFIIEalpha HTH domainDomain
HA [auth h]IPR002853Transcription initiation factor IIE subunit alpha, N-terminalDomain
KA [auth k]IPR007081RNA polymerase Rpb1, domain 5Domain
KA [auth k]IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
KA [auth k]IPR007075RNA polymerase Rpb1, domain 6Domain
KA [auth k]IPR000684RNA polymerase II, heptapeptide repeat, eukaryoticRepeat
KA [auth k]IPR007083RNA polymerase Rpb1, domain 4Domain
KA [auth k]IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
KA [auth k]IPR006592RNA polymerase, N-terminalDomain
KA [auth k]IPR007066RNA polymerase Rpb1, domain 3Domain
KA [auth k]IPR007073RNA polymerase Rpb1, domain 7Domain
KA [auth k]IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
KA [auth k]IPR038593RNA polymerase Rpb1, domain 7 superfamilyHomologous Superfamily
KA [auth k]IPR000722RNA polymerase, alpha subunitDomain
KA [auth k]IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
KA [auth k]IPR007080RNA polymerase Rpb1, domain 1Domain
NA [auth n]IPR027353NET domainDomain
NA [auth n]IPR016665SAS complex subunit SAS5/transcription initiation factor TFIID subunit 14Family
NA [auth n]IPR038704YEATS superfamilyHomologous Superfamily
NA [auth n]IPR005033YEATSFamily
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
IPR007018Mediator complex, subunit Med6Family
IPR016612Mediator complex, subunit Med6, fungiFamily
IPR038566Mediator complex, subunit Med6 superfamilyHomologous Superfamily
IPR019364Mediator complex, subunit Med8, fungi/metazoaFamily
IPR013921Mediator complex, subunit Med20Family
IPR016532Mediator of RNA polymerase II transcription subunit 20Family
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
IPR037212Mediator complex, subunit Med7/Med21-likeHomologous Superfamily
IPR009244Mediator complex, subunit Med7Family
IPR044888Mediator complex, subunit Med7 superfmailyHomologous Superfamily
IPR011425Mediator of RNA polymerase II transcription subunit 9Family
IPR037212Mediator complex, subunit Med7/Med21-likeHomologous Superfamily
IPR021384Mediator complex, subunit Med21Family
IPR008831Mediator complex, subunit Med31Family
IPR038089Mediator of RNA polymerase II, subunit Med31 superfamilyHomologous Superfamily
IPR010643Helical and beta-bridge domainDomain
IPR001945RAD3/XPD familyFamily
IPR045028Helicase superfamily 1/2, DinG/Rad3-likeFamily
IPR002464DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved siteConserved Site
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
IPR042493Bacterial type XPD DNA helicase, FeS cluster domainHomologous Superfamily
IPR006554Helicase-like, DEXD box c2 typeDomain
IPR006555ATP-dependent helicase, C-terminalDomain
IPR010614RAD3-like helicase, DEADDomain
IPR014013Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-typeDomain
IPR013020ATP-dependent helicase Rad3/Chl1-likeFamily
IPR032830Helicase XPB/Ssl2, N-terminal domainDomain
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
IPR006935Helicase/UvrB, N-terminalDomain
IPR001650Helicase, C-terminal domain-likeDomain
IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
IPR032438ERCC3/RAD25/XPB helicase, C-terminal domainDomain
IPR001161Helicase XPB/Ssl2Family
CA [auth c]IPR000812Transcription factor TFIIBFamily
CA [auth c]IPR023486Transcription factor TFIIB, conserved siteConserved Site
CA [auth c]IPR013150Transcription factor TFIIB, cyclin-like domainDomain
CA [auth c]IPR013137Zinc finger, TFIIB-typeDomain
CA [auth c]IPR036915Cyclin-like superfamilyHomologous Superfamily
CA [auth c]IPR013763Cyclin-like domainDomain
IPR011262DNA-directed RNA polymerase, insert domainDomain
IPR011263DNA-directed RNA polymerase, RpoA/D/Rpb3-typeDomain
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
DA [auth d]IPR004855Transcription factor IIA, alpha/beta subunitFamily
DA [auth d]IPR009088Transcription factor IIA, beta-barrelHomologous Superfamily
EA [auth e]IPR015871Transcription initiation factor IIA, gamma subunit, C-terminalDomain
EA [auth e]IPR015872Transcription initiation factor IIA, gamma subunit, N-terminalDomain
EA [auth e]IPR009083Transcription factor IIA, alpha-helical domainHomologous Superfamily
EA [auth e]IPR009088Transcription factor IIA, beta-barrelHomologous Superfamily
EA [auth e]IPR003194Transcription initiation factor IIA, gamma subunitFamily
IA [auth i]IPR040501TFA2, Winged helix domain 2Domain
IA [auth i]IPR016656Transcription initiation factor TFIIE, beta subunitFamily
IA [auth i]IPR003166Transcription factor TFIIE beta subunit, DNA-binding domainDomain
JA [auth j]IPR030491TATA-box binding protein, conserved siteConserved Site
JA [auth j]IPR000814TATA-box binding proteinFamily
JA [auth j]IPR012295TBP domain superfamilyHomologous Superfamily
JA [auth j]IPR033710TATA-box binding protein, eukaryoticFamily
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
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