8WAU

De novo transcribing complex 11 (TC11), the early elongation complex with Pol II positioned 11nt downstream of TSS


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
C [auth T]SCOP2B SuperfamilyRap30/74 heterodimerisation domain-like8003550 3000142 SCOP2B (2022-06-29)
L [auth t]SCOP2B SuperfamilyRPB6/omega subunit-like8106082 3000189 SCOP2B (2022-06-29)
Q [auth y]SCOP2B SuperfamilyRBP11-like subunits of RNA polymerase8080728 3001655 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
C [auth T]PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
C [auth T]PF17683TFIIF, beta subunit N-terminus (TFIIF_beta_N)TFIIF, beta subunit N-terminus- Family
D [auth X]PF01194RNA polymerases N / 8 kDa subunit (RNA_pol_N)RNA polymerases N / 8 kDa subunit- Domain
E [auth Y]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 Y]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
B [auth S]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
B [auth S]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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth N]Alpha-amanitin - -
C [auth T]General transcription factor IIF subunit 2
D [auth X]non-template DNA---
E [auth Y]template DNA---
I [auth q]DNA-directed RNA polymerase II subunit RPB3 -
J [auth r]DNA-directed RNA polymerase II subunit RPB4
K [auth s]DNA-directed RNA polymerase II subunit E
L [auth t]DNA-directed RNA polymerase II subunit F
N [auth v]DNA-directed RNA polymerases I, II, and III subunit RPABC3 -
Q [auth y]DNA-directed RNA polymerase II subunit RPB11-a -
M [auth u]DNA-directed RNA polymerase II subunit RPB7
O [auth w]DNA-directed RNA polymerase II subunit RPB9
P [auth x]DNA-directed RNA polymerases I, II, and III subunit RPABC5
R [auth z]RPB12 -
B [auth S]General transcription factor IIF subunit 1
F [auth Z]RNA---
G [auth o]DNA-directed RNA polymerase subunit -
H [auth p]DNA-directed RNA polymerase subunit beta -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
C [auth T]IPR003196Transcription initiation factor IIF, beta subunitFamily
C [auth T]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
C [auth T]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
C [auth T]IPR040450TFIIF beta subunit, HTH domainDomain
C [auth T]IPR040504TFIIF, beta subunit, N-terminalDomain
C [auth T]IPR011039Transcription Factor IIF, Rap30/Rap74, interactionHomologous Superfamily
I [auth q]IPR011262DNA-directed RNA polymerase, insert domainDomain
I [auth q]IPR011263DNA-directed RNA polymerase, RpoA/D/Rpb3-typeDomain
I [auth q]IPR036643DNA-directed RNA polymerase, insert domain superfamilyHomologous Superfamily
I [auth q]IPR022842DNA-directed RNA polymerase subunit Rpo3/Rpb3/RPAC1Family
I [auth q]IPR001514DNA-directed RNA polymerase, 30-40kDa subunit, conserved siteConserved Site
I [auth q]IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
J [auth r]IPR005574RNA polymerase subunit Rpb4/RPC9Family
J [auth r]IPR010997HRDC-like superfamilyHomologous Superfamily
J [auth r]IPR006590RNA polymerase Rpb4/RPC9, coreDomain
J [auth r]IPR038324Rpb4/RPC9 superfamilyHomologous Superfamily
J [auth r]IPR045222DNA-directed RNA polymerase II subunit Rpb4-likeFamily
K [auth s]IPR014381DNA-directed RNA polymerase subunit Rpo5/Rpb5Family
K [auth s]IPR036710RNA polymerase Rpb5, N-terminal domain superfamilyHomologous Superfamily
K [auth s]IPR035913RPB5-like RNA polymerase subunit superfamilyHomologous Superfamily
K [auth s]IPR000783RNA polymerase, subunit H/Rpb5 C-terminalDomain
K [auth s]IPR020608RNA polymerase, subunit H/Rpb5, conserved siteConserved Site
K [auth s]IPR005571RNA polymerase, Rpb5, N-terminalDomain
L [auth t]IPR020708DNA-directed RNA polymerase, 14-18kDa subunit, conserved siteConserved Site
L [auth t]IPR028363DNA-directed RNA polymerase, subunit RPB6Family
L [auth t]IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
L [auth t]IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
L [auth t]IPR006111Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunitFamily
N [auth v]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
N [auth v]IPR005570DNA-directed RNA polymerases I, II, and III subunit RPABC3Family
Q [auth y]IPR022905DNA-directed RNA polymerase subunit Rpo11-likeFamily
Q [auth y]IPR009025DNA-directed RNA polymerase, RBP11-like dimerisation domainDomain
Q [auth y]IPR036603RNA polymerase, RBP11-like subunitHomologous Superfamily
Q [auth y]IPR008193DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved siteConserved Site
Q [auth y]IPR037685RNA polymerase RBP11Family
M [auth u]IPR003029S1 domainDomain
M [auth u]IPR045113RNA polymerase subunit Rpb7-likeFamily
M [auth u]IPR005576RNA polymerase Rpb7-like , N-terminalDomain
M [auth u]IPR036898RNA polymerase Rpb7-like, N-terminal domain superfamilyHomologous Superfamily
M [auth u]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
O [auth w]IPR012164DNA-directed RNA polymerase subunit/transcription factor SFamily
O [auth w]IPR001222Zinc finger, TFIIS-typeDomain
O [auth w]IPR034012Pol II subunit B9, C-terminal zinc ribbonDomain
O [auth w]IPR019761DNA-directed RNA polymerase M, 15kDa subunit, conserved siteConserved Site
O [auth w]IPR001529DNA-directed RNA polymerase, M/15kDa subunitDomain
P [auth x]IPR023580RNA polymerase subunit RPB10Homologous Superfamily
P [auth x]IPR020789RNA polymerases, subunit N, zinc binding siteBinding Site
P [auth x]IPR000268DNA-directed RNA polymerase subunit RPABC5/Rpb10Family
R [auth z]IPR006591RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4Family
R [auth z]IPR029040RNA polymerase subunit RPABC4/transcription elongation factor Spt4Homologous Superfamily
R [auth z]IPR039747DNA-directed RNA polymerases I, II, and III subunit RPABC4Family
B [auth S]IPR008851Transcription initiation factor IIF, alpha subunitFamily
B [auth S]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
B [auth S]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
B [auth S]IPR011039Transcription Factor IIF, Rap30/Rap74, interactionHomologous Superfamily
G [auth o]IPR007066RNA polymerase Rpb1, domain 3Domain
G [auth o]IPR007081RNA polymerase Rpb1, domain 5Domain
G [auth o]IPR007073RNA polymerase Rpb1, domain 7Domain
G [auth o]IPR045867DNA-directed RNA polymerase, subunit beta-primeFamily
G [auth o]IPR042102RNA polymerase Rpb1, domain 3 superfamilyHomologous Superfamily
G [auth o]IPR007075RNA polymerase Rpb1, domain 6Domain
G [auth o]IPR000684RNA polymerase II, heptapeptide repeat, eukaryoticRepeat
G [auth o]IPR007083RNA polymerase Rpb1, domain 4Domain
G [auth o]IPR038593RNA polymerase Rpb1, domain 7 superfamilyHomologous Superfamily
G [auth o]IPR000722RNA polymerase, alpha subunitDomain
G [auth o]IPR044893RNA polymerase Rpb1, clamp domain superfamilyHomologous Superfamily
G [auth o]IPR038120RNA polymerase Rpb1, funnel domain superfamilyHomologous Superfamily
G [auth o]IPR006592RNA polymerase, N-terminalDomain
G [auth o]IPR007080RNA polymerase Rpb1, domain 1Domain
H [auth p]IPR007642RNA polymerase Rpb2, domain 2Domain
H [auth p]IPR015712DNA-directed RNA polymerase, subunit 2Family
H [auth p]IPR037033DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamilyHomologous Superfamily
H [auth p]IPR037034RNA polymerase Rpb2, domain 2 superfamilyHomologous Superfamily
H [auth p]IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
H [auth p]IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
H [auth p]IPR007645RNA polymerase Rpb2, domain 3Domain
H [auth p]IPR007646RNA polymerase Rpb2, domain 4Domain
H [auth p]IPR007647RNA polymerase Rpb2, domain 5Domain
H [auth p]IPR014724RNA polymerase Rpb2, OB-foldHomologous Superfamily
H [auth p]IPR007644RNA polymerase, beta subunit, protrusionDomain
H [auth p]IPR007641RNA polymerase Rpb2, domain 7Domain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
C [auth T]PharosP13984

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
A [auth N]CSX Parent Component: CYS

RESIDAA0451

PSI-MOD :  2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380
A [auth N]HYP Parent Component: PRO

RESIDAA0451 , AA0030

PSI-MOD :  2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380 , 4-hydroxy-L-proline MOD:00039
A [auth N]ILX Parent Component: ILE

RESIDAA0451 , AA0030 , AA0449

PSI-MOD :  2'-(S-L-cysteinyl)-6'-hydroxy-L-tryptophan sulfoxide MOD:01380 , 4-hydroxy-L-proline MOD:00039 , (2S,3R,4R)-4,5-dihydroxyisoleucine MOD:01378
A [auth N]TRX Parent Component: TRP

RESIDAA0451 , AA0030 , AA0449

F [auth Z]ATP RESIDAA0451 , AA0030 , AA0449

F [auth Z]G2L Parent Component: G

RESIDAA0451 , AA0030 , AA0449