9FD2 | pdb_00009fd2

Structure of Pol II-TC-NER-STK19 complex


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
KSCOP2B SuperfamilyRBP11-like subunits of RNA polymerase 8080728 3001655 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyRNA polymerase subunits 8103068 3001823 SCOP2B (2022-06-29)
R [auth b]SCOP2B SuperfamilyWD40 repeat-like 8051194 3001694 SCOP2B (2022-06-29)
R [auth b]SCOP2B SuperfamilyWD40 repeat-like 8052530 3001694 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRPB6/omega subunit-like 8106082 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 ...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 ...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 ...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 ...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 ...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 ...Domain
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
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 dom ...Domain
PF01194RNA polymerases N / 8 kDa subunit (RNA_pol_N)RNA polymerases N / 8 kDa subunitDomain
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 ...Domain
PF03604DNA directed RNA polymerase, 7 kDa subunit (Zn_ribbon_RPAB4)DNA directed RNA polymerase, 7 kDa subunitDomain
PF10433RSE1/DDB1/CPSF1 first beta-propeller (Beta-prop_RSE1_1st)RSE1/DDB1/CPSF1 first beta-propeller- Repeat
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 ...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 ...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 ...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 ...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 ...Domain
PF03178CPSF A subunit region (CPSF_A)CPSF A subunit region- Repeat
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 ...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 ...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 archaeal Domain
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 ...Domain
PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
PF10494Serine-threonine protein kinase 19 (Stk19)Serine-threonine protein kinase 19- 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 ...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 (Zn_ribbon_RPB9)RNA polymerases M/15 Kd subunitDomain
PF01096Transcription factor S-II (TFIIS) (Zn_ribbon_TFIIS)Transcription factor S-II (TFIIS)Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
DNA-directed RNA polymerase subunit
DNA-directed RNA polymerases I, II, and III subunit RPABC5
DNA-directed RNA polymerase II subunit RPB11-a -
RNA polymerase II, I and III subunit K
M [auth f]Transcription elongation factor 1 homolog
Non-template DNA---
O [auth M]RNA---
P [auth T]Template DNA---
Q [auth a]DNA excision repair protein ERCC-8-
R [auth b]DNA damage-binding protein 1
S [auth c]DET1- and DDB1-associated protein 1-
DNA-directed RNA polymerase subunit beta -
T [auth g]Inactive serine/threonine-protein kinase 19
U [auth e]DNA excision repair protein ERCC-6
V [auth d]UV-stimulated scaffold protein A
DNA-directed RNA polymerase II subunit RPB3
RNA polymerase II subunit D
DNA-directed RNA polymerase II subunit E
DNA-directed RNA polymerases I, II, and III subunit RPABC2
DNA-directed RNA polymerase subunit
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
IPR007066RNA polymerase Rpb1, domain 3Domain
IPR007081RNA polymerase Rpb1, domain 5Domain
IPR007073RNA polymerase Rpb1, domain 7Domain
IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
IPR007075RNA polymerase Rpb1, domain 6Domain
IPR000684RNA polymerase II, heptapeptide repeat, eukaryoticRepeat
IPR007083RNA polymerase Rpb1, domain 4Domain
IPR038593RNA polymerase Rpb1, domain 7 superfamilyHomologous Superfamily
IPR000722RNA polymerase, alpha subunitDomain
IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
IPR006592RNA polymerase, N-terminalDomain
IPR007080RNA polymerase Rpb1, domain 1Domain
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
M [auth f]IPR007808Transcription elongation factor 1Family
M [auth f]IPR038567Transcription elongation factor 1 superfamilyHomologous Superfamily
Q [auth a]IPR019775WD40 repeat, conserved siteConserved Site
Q [auth a]IPR042238DNA excision repair protein Rad28/ERCC8/Ckn1/ATCSA-1Family
Q [auth a]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
Q [auth a]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
Q [auth a]IPR001680WD40 repeatRepeat
Q [auth a]IPR020472G-protein beta WD-40 repeatRepeat
R [auth b]IPR018846RSE1/DDB1/CPSF1, first beta-propeller domainDomain
R [auth b]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
R [auth b]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
R [auth b]IPR004871Cleavage/polyadenylation specificity factor, A subunit, C-terminalDomain
R [auth b]IPR050358RSE1/DDB1/CFT1/CPSF1Family
S [auth c]IPR018276DET1- and DDB1-associated protein 1 domainDomain
S [auth c]IPR033575DET1- and DDB1-associated protein 1-likeFamily
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
T [auth g]IPR018865Inactive serine/threonine-protein kinase 19-likeFamily
U [auth e]IPR049730SNF2/RAD5-like, C-terminal helicase domainDomain
U [auth e]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
U [auth e]IPR001650Helicase, C-terminal domain-likeDomain
U [auth e]IPR014001Helicase superfamily 1/2, ATP-binding domainDomain
U [auth e]IPR000330SNF2, N-terminalDomain
U [auth e]IPR050496SNF2/RAD54 Helicase and DNA RepairFamily
U [auth e]IPR038718SNF2-like, N-terminal domain superfamilyHomologous Superfamily
V [auth d]IPR018610UV-stimulated scaffold protein AFamily
V [auth d]IPR008942ENTH/VHSHomologous Superfamily
V [auth d]IPR049408UV-stimulated scaffold protein A, N-terminal alpha-solenoid repeatsRepeat
V [auth d]IPR049431UV-stimulated scaffold protein A, C-terminal domainDomain
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
IPR036710RNA polymerase Rpb5, N-terminal domain superfamilyHomologous Superfamily
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
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
IPR003029S1 domainDomain
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
IPR001529DNA-directed RNA polymerase II subunit RPB9-like, zinc ribbonDomain
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

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
M [auth f]PharosP60002
Q [auth a]PharosQ13216
R [auth b]PharosQ16531
S [auth c]PharosQ9BW61
T [auth g]PharosP49842
U [auth e]PharosQ03468
V [auth d]PharosQ2YD98