9RZD | pdb_00009rzd

State 3 MAP 2 SPT6 with SETD2


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth D]SCOP2B SuperfamilyHRDC-like 8101241 3000132 SCOP2B (2022-06-29)
D [auth Z]SCOP2B SuperfamilyTranslation proteins SH3-like KOW motif containing domain 8039849 3000334 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth D]PF03874RNA polymerase Rpb4 (RNA_pol_Rpb4)RNA polymerase Rpb4- Family
D [auth Z]PF00467KOW motif (KOW)KOW motif- Family
E [auth M]PF14639Holliday-junction resolvase-like of SPT6 (YqgF)Holliday-junction resolvase-like of SPT6The YqgF domain of SPT6 proteins is homologous to the E.coli RuvC [1] but its putative catalytic site lacks the carboxylate side chains critical for coordinating magnesium ions that mediate phosphodiester bond-cleavage [2] Domain
E [auth M]PF17674HHH domain (HHH_9)HHH domainDomain
E [auth M]PF22706Tex central region-like (Tex_central_region)Tex central region-likeThis domain is found in Tex protein and other related proteins. Tex belongs to a family of prokaryotic transcriptional accessory factors that likely function in a variety of transcriptional processes [1-5].This domain is mainly helical, consisting of ...This domain is found in Tex protein and other related proteins. Tex belongs to a family of prokaryotic transcriptional accessory factors that likely function in a variety of transcriptional processes [1-5].This domain is mainly helical, consisting of a number of small helices that wrap around a long central helix.
Domain
E [auth M]PF14641Helix-turn-helix DNA-binding domain of SPT6 (HTH_44)Helix-turn-helix DNA-binding domain of SPT6This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins. Domain
E [auth M]PF14633SH2 domain (SH2_2)SH2 domainDomain
E [auth M]PF14635Helix-hairpin-helix motif (HHH_7)Helix-hairpin-helix motifDomain
B [auth G]PF03876SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N)SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at leas ...Rpb7 bind to Rpb4 to form a heterodimer. This complex is thought to interact with the nascent RNA strand during RNA polymerase II elongation[1]. This family includes the homologs from RNA polymerase I and III. In RNA polymerase I, Rpa43 is at least one of the subunits contacted by the transcription factor TIF-IA [2]. The N terminus of Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved in protein-protein interaction [3].
Domain
B [auth G]PF00575S1 RNA binding domain (S1)S1 RNA binding domainThe S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure. Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth D]RNA polymerase II subunit D
C [auth O]Histone-lysine N-methyltransferase SETD2
D [auth Z]Transcription elongation factor SPT5
E [auth M]Transcription elongation factor SPT6
B [auth G]DNA-directed RNA polymerase II subunit RPB7

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth D]IPR005574RNA polymerase subunit Rpb4/RPC9Family
A [auth D]IPR010997HRDC-like superfamilyHomologous Superfamily
A [auth D]IPR006590RNA polymerase Rpb4/RPC9, coreDomain
A [auth D]IPR038324Rpb4/RPC9 superfamilyHomologous Superfamily
A [auth D]IPR045222DNA-directed RNA polymerase II subunit Rpb4-likeFamily
C [auth O]IPR006560AWS domainDomain
C [auth O]IPR046341SET domain superfamilyHomologous Superfamily
C [auth O]IPR001214SET domainDomain
C [auth O]IPR036020WW domain superfamilyHomologous Superfamily
C [auth O]IPR003616Post-SET domainDomain
C [auth O]IPR035441TFIIS/LEDGF domain superfamilyHomologous Superfamily
C [auth O]IPR044437SETD2/Set2, SET domainDomain
C [auth O]IPR038190Set2 Rpb1 interacting domain superfamilyHomologous Superfamily
C [auth O]IPR001202WW domainDomain
C [auth O]IPR042294Histone-lysine N-methyltransferase SETD2, animalFamily
C [auth O]IPR013257Set2 Rpb1 interacting domainDomain
D [auth Z]IPR041976Spt5, KOW domain repeat 3Domain
D [auth Z]IPR041980Spt5, KOW domain repeat 6, metazoaDomain
D [auth Z]IPR039385NGN domain, eukaryoticDomain
D [auth Z]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
D [auth Z]IPR022581Spt5 transcription elongation factor, N-terminalDomain
D [auth Z]IPR024945Spt5 C-terminal domainDomain
D [auth Z]IPR006645NusG-like, N-terminalDomain
D [auth Z]IPR041975Spt5, KOW domain repeat 2Domain
D [auth Z]IPR039659Transcription elongation factor SPT5Family
D [auth Z]IPR036735NusG, N-terminal domain superfamilyHomologous Superfamily
D [auth Z]IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
D [auth Z]IPR041973Spt5, KOW domain repeat 1Domain
D [auth Z]IPR005100NGN domainDomain
D [auth Z]IPR041977Spt5, KOW domain repeat 4Domain
D [auth Z]IPR017071Transcription elongation factor Spt5, eukaryoteFamily
D [auth Z]IPR005824KOWDomain
D [auth Z]IPR041978Spt5, KOW domain repeat 5Domain
E [auth M]IPR042066Spt6, Death-like domainHomologous Superfamily
E [auth M]IPR028231Transcription elongation factor Spt6, YqgF domainDomain
E [auth M]IPR037027YqgF/RNase H-like domain superfamilyHomologous Superfamily
E [auth M]IPR036860SH2 domain superfamilyHomologous Superfamily
E [auth M]IPR000980SH2 domainDomain
E [auth M]IPR006641YqgF/RNase H-like domainDomain
E [auth M]IPR041692HHH domain 9Domain
E [auth M]IPR010994RuvA domain 2-likeHomologous Superfamily
E [auth M]IPR023319Tex-like protein, HTH domain superfamilyHomologous Superfamily
E [auth M]IPR012337Ribonuclease H-like superfamilyHomologous Superfamily
E [auth M]IPR017072Transcription elongation factor Spt6Family
E [auth M]IPR035420Spt6, SH2 domainDomain
E [auth M]IPR032706Transcription elongation factor Spt6, helix-hairpin-helix motifDomain
E [auth M]IPR003029S1 domainDomain
E [auth M]IPR023323Tex-like domain superfamilyHomologous Superfamily
E [auth M]IPR055179Tex-like, central regionDomain
E [auth M]IPR028088Helix-turn-helix DNA-binding domain of Spt6Domain
E [auth M]IPR035019Spt6, SH2 domain, N terminusDomain
E [auth M]IPR035018Spt6, SH2 domain, C terminusDomain
E [auth M]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
E [auth M]IPR028083Spt6 acidic, N-terminal domainDomain
B [auth G]IPR036898RNA polymerase Rpb7-like, N-terminal domain superfamilyHomologous Superfamily
B [auth G]IPR003029S1 domainDomain
B [auth G]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
B [auth G]IPR045113RNA polymerase subunit Rpb7-likeFamily
B [auth G]IPR005576RNA polymerase Rpb7-like , N-terminalDomain