9EH2 | pdb_00009eh2

RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream

External Resource: Annotation


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
FSCOP2B SuperfamilyRPB6/omega subunit-like 8106082 3000189 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyRNA polymerase subunits 8103068 3001823 SCOP2B (2022-06-29)
BA [auth b]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
DA [auth f]SCOP2B SuperfamilyCore histone-like 8042439 3001387 SCOP2B (2022-06-29)
FA [auth h]SCOP2B SuperfamilyCore histone-like 8041279 3001387 SCOP2B (2022-06-29)
HA [auth x]SCOP2B SuperfamilyPH domain-like 8103657 3000134 SCOP2B (2022-06-29)
HA [auth x]SCOP2B SuperfamilyPH domain-like 8103651 3000134 SCOP2B (2022-06-29)
IA [auth y]SCOP2B SuperfamilyPH domain-like 8084337 3000134 SCOP2B (2022-06-29)
IA [auth y]SCOP2B SuperfamilyPH domain-like 8103658 3000134 SCOP2B (2022-06-29)
EA [auth g]SCOP2B SuperfamilyCore histone-like 8041278 3001387 SCOP2B (2022-06-29)
ZSCOP2B SuperfamilyTranslation proteins SH3-like KOW motif containing domain 8039849 3000334 SCOP2B (2022-06-29)
RSCOP2B SuperfamilyPlus3-like 8033751 3000248 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
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 dom ...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
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
PF15511Centromere kinetochore component CENP-T histone fold (CENP-T_C)Centromere kinetochore component CENP-T histone foldCENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].
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
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 archaeal Domain
PF01192RNA polymerase Rpb6 (RNA_pol_Rpb6)RNA polymerase Rpb6- Family
PF15511Centromere kinetochore component CENP-T histone fold (CENP-T_C)Centromere kinetochore component CENP-T histone foldCENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly asso ...CENP-T is a family of vertebral kinetochore proteins that associates directly with CENP-W. The N-terminus of CENP-T proteins interacts directly with the Ndc80 complex in the outer kinetochore. Importantly, the CENP-T-W complex does not directly associate with CENP-A, but with histone H3 in the centromere region. CENP-T and -W form a hetero-tetramer with CENP-S and -X and bind to a ~100 bp region of nucleosome-free DNA forming a nucleosome-like structure. The DNA-CENP-T-W-S-X complex is likely to be associated with histone H3-containing nucleosomes rather than with CENP-nucleosomes. This domain is the C-terminal histone fold domain of CENP-T, which associates with chromatin [2-3].
Domain
PF16211C-terminus of histone H2A (Histone_H2A_C)C-terminus of histone H2A- 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 (Zn_ribbon_RPB9)RNA polymerases M/15 Kd subunitDomain
PF01096Transcription factor S-II (TFIIS) (Zn_ribbon_TFIIS)Transcription factor S-II (TFIIS)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 ...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 (Zn_ribbon_RPAB4)DNA directed RNA polymerase, 7 kDa subunitDomain
PF08711TFIIS helical bundle-like domain (Med26)TFIIS helical bundle-like domainMediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail a ...Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function [3]. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. Notably, the 'small' and 'large' Mediator complexes differ in their subunit composition: the Med26 subunit preferentially associates with the small, active complex, whereas cdk8, cyclin C, Med12 and Med13 associate with the large Mediator complex [4]. This family includesthe C terminal region of a number of eukaryotic hypothetical proteins which are homologous to the Saccharomyces cerevisiae protein IWS1. IWS1 is known to be an Pol II transcription elongation factor and interacts with Spt6 and Spt5 [5,6].
Domain
PF13181Tetratricopeptide repeat (TPR_8)Tetratricopeptide repeat- Repeat
PF13374Tetratricopeptide repeat (TPR_10)Tetratricopeptide repeat- Repeat
PF01096Transcription factor S-II (TFIIS) (Zn_ribbon_TFIIS)Transcription factor S-II (TFIIS)Domain
PF07500Transcription factor S-II (TFIIS), central domain (TFIIS_M)Transcription factor S-II (TFIIS), central domainTranscription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is compo ...Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III), this domain and Pfam:PF01096 are required for transcription activity [1].
Domain
PF03985Paf1 (Paf1)Paf1- Family
PF08644FACT complex subunit (SPT16/CDC68) (SPT16)FACT complex subunit (SPT16/CDC68)Proteins in this family are subunits the FACT complex. The FACT complex plays a role in transcription initiation and promotes binding of TATA-binding protein (TBP) to a TATA box in chromatin [2]. Domain
PF03531Structure-specific recognition protein (SSRP1) (SSrecog)Structure-specific recognition protein (SSRP1)SSRP1 has been implicated in transcriptional initiation and elongation and in DNA replication and repair [1]. This domain belongs to the Pleckstrin homology fold superfamily. Domain
PF17292POB3-like N-terminal PH domain (POB3_N)POB3-like N-terminal PH domainThis domain is found at the N-terminus of POB3 and related proteins. Domain
PF06093Spt4/RpoE2 zinc finger (Spt4)Spt4/RpoE2 zinc fingerThis family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 [2]. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via ...This family consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 [2]. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles [1]. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in [3]. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery.
Domain
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
PF03439Early transcription elongation factor of RNA pol II, NGN section (Spt5-NGN)Early transcription elongation factor of RNA pol II, NGN section- Family
PF00467KOW motif (KOW)KOW motif- Family
PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
PF04004Leo1-like protein (Leo1)Leo1-like protein- Family
PF03126Plus-3 domain (Plus-3)Plus-3 domainThis domain is about 90 residues in length and is often found associated with the Pfam:PF02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged ...This domain is about 90 residues in length and is often found associated with the Pfam:PF02213 domain. The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor [1].
Domain
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
PF17674HHH domain (HHH_9)HHH domainDomain
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
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
PF14633SH2 domain (SH2_2)SH2 domainDomain
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
PF14635Helix-hairpin-helix motif (HHH_7)Helix-hairpin-helix motifDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
DNA-directed RNA polymerase subunit
DNA-directed RNA polymerase subunit beta
DNA-directed RNA polymerase II subunit RPB3
DNA-directed RNA polymerases I, II, and III subunit RPABC2
DNA-directed RNA polymerase II subunit RPB7
DNA-directed RNA polymerases I, II, and III subunit RPABC3
DNA-directed RNA polymerase II subunit RPB9
DNA-directed RNA polymerases I, II, and III subunit RPABC5
RNA polymerase II subunit J
RNA polymerase II subunit K
Protein IWS1 homolog-
RNA---
RNA polymerase-associated protein CTR9 homolog
Transcription elongation factor A protein 1
Template DNA---
RNA polymerase II-associated factor 1 homolog
Parafibromin
Transcription elongation factor SPT4
BA [auth b],
DA [auth f]		Histone H4
FA [auth h]Histone H2B 1.1 -
GA [auth l]Histone-lysine N-methyltransferase SETD2
HA [auth x]FACT complex subunit SPT16
IA [auth y]FACT complex subunit SSRP1
DNA-directed RNA polymerase II subunit E
RNA polymerase Rpb4/RPC9 core domain-containing protein---
EA [auth g]Histone H2A type 1
AA [auth a],
CA [auth e]		Histone H3 -
Transcription elongation factor SPT5
WDR61-
RNA polymerase-associated protein LEO1
RNA polymerase-associated protein RTF1 homolog
non-template DNA---
Transcription elongation factor SPT6

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
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
IPR007120DNA-directed RNA polymerase, subunit 2, hybrid-binding domainDomain
IPR007121RNA polymerase, beta subunit, conserved siteConserved Site
IPR007645RNA polymerase Rpb2, domain 3Domain
IPR007646RNA polymerase Rpb2, domain 4Domain
IPR007647RNA polymerase Rpb2, domain 5Domain
IPR014724RNA polymerase Rpb2, OB-foldHomologous Superfamily
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
IPR020708DNA-directed RNA polymerase, 14-18kDa subunit, conserved siteConserved Site
IPR028363DNA-directed RNA polymerase, subunit RPB6Family
IPR006110RNA polymerase, subunit omega/Rpo6/RPB6Family
IPR036161RPB6/omega subunit-like superfamilyHomologous Superfamily
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
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
IPR035441TFIIS/LEDGF domain superfamilyHomologous Superfamily
IPR017923Transcription factor IIS, N-terminalDomain
IPR051037RNA Polymerase II Transcription Factor IWS1Family
IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
IPR031101RNA polymerase-associated protein Ctr9Family
IPR019734Tetratricopeptide repeatRepeat
IPR006289Transcription elongation factor, TFIISFamily
IPR001222Zinc finger, TFIIS-typeDomain
IPR003618Transcription elongation factor S-II, central domainDomain
IPR035441TFIIS/LEDGF domain superfamilyHomologous Superfamily
IPR036575Transcription elongation factor S-II, central domain superfamilyHomologous Superfamily
IPR035100Transcription elongation factor, IIS-typeFamily
IPR017923Transcription factor IIS, N-terminalDomain
IPR003617Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-typeDomain
IPR007133RNA polymerase II associated factor Paf1Family
IPR038103Cell division control protein 73, C-terminal domain superfamilyHomologous Superfamily
IPR031336Cell division control protein 73, C-terminalDomain
IPR007852Cdc73/ParafibrominFamily
IPR032041Paf1 complex subunit Cdc73, N-terminal domainDomain
IPR038510Spt4 superfamilyHomologous Superfamily
IPR009287Transcription initiation Spt4Family
IPR029040RNA polymerase subunit RPABC4/transcription elongation factor Spt4Homologous Superfamily
IPR022800Spt4/RpoE2 zinc fingerDomain
BA [auth b],
DA [auth f]		IPR009072Histone-foldHomologous Superfamily
BA [auth b],
DA [auth f]		IPR001951Histone H4Family
BA [auth b],
DA [auth f]		IPR035425CENP-T/Histone H4, histone foldDomain
BA [auth b],
DA [auth f]		IPR019809Histone H4, conserved siteConserved Site
BA [auth b],
DA [auth f]		IPR004823TATA box binding protein associated factor (TAF), histone-like fold domainDomain
FA [auth h]IPR009072Histone-foldHomologous Superfamily
FA [auth h]IPR055333Histone H2B, conserved siteConserved Site
FA [auth h]IPR000558Histone H2BFamily
FA [auth h]IPR007125Core Histone H2A/H2B/H3 domainDomain
GA [auth l]IPR006560AWS domainDomain
GA [auth l]IPR046341SET domain superfamilyHomologous Superfamily
GA [auth l]IPR001214SET domainDomain
GA [auth l]IPR036020WW domain superfamilyHomologous Superfamily
GA [auth l]IPR003616Post-SET domainDomain
GA [auth l]IPR035441TFIIS/LEDGF domain superfamilyHomologous Superfamily
GA [auth l]IPR044437SETD2/Set2, SET domainDomain
GA [auth l]IPR038190Set2 Rpb1 interacting domain superfamilyHomologous Superfamily
GA [auth l]IPR001202WW domainDomain
GA [auth l]IPR042294Histone-lysine N-methyltransferase SETD2, animalFamily
GA [auth l]IPR013257Set2 Rpb1 interacting domainDomain
HA [auth x]IPR033825FACT complex subunit Spt16, peptidase M24-like domainDomain
HA [auth x]IPR048969FACT complex subunit SPT16, C-terminal domainDomain
HA [auth x]IPR029149Creatinase/Aminopeptidase P/Spt16, N-terminalHomologous Superfamily
HA [auth x]IPR011993PH-like domain superfamilyHomologous Superfamily
HA [auth x]IPR013719Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domainDomain
HA [auth x]IPR040258FACT complex subunit Spt16Family
HA [auth x]IPR013953FACT complex subunit SPT16, middle domainDomain
HA [auth x]IPR029148FACT complex subunit SPT16, N-terminal lobe domainDomain
HA [auth x]IPR056595FACT complex subunit SPT16, PH-like domainDomain
HA [auth x]IPR036005Creatinase/aminopeptidase-likeHomologous Superfamily
HA [auth x]IPR000994Peptidase M24Domain
IA [auth y]IPR038167SSRP1 domain superfamilyHomologous Superfamily
IA [auth y]IPR048985FACT complex subunit SSRP1, C-terminal domainDomain
IA [auth y]IPR050454RTT106/SSRP1 Histone Chaperone/FACT ComplexFamily
IA [auth y]IPR035417FACT complex subunit SSRP1/POB3, N-terminal PH domainDomain
IA [auth y]IPR000969FACT complex subunit SSRP1/POB3Family
IA [auth y]IPR011993PH-like domain superfamilyHomologous Superfamily
IA [auth y]IPR013719Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domainDomain
IA [auth y]IPR048993FACT complex subunit SSRP1-like, first PH domainDomain
IA [auth y]IPR024954SSRP1, dimerization domainDomain
IA [auth y]IPR009071High mobility group box domainDomain
IA [auth y]IPR036910High mobility group box domain superfamilyHomologous Superfamily
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
EA [auth g]IPR009072Histone-foldHomologous Superfamily
EA [auth g]IPR002119Histone H2AFamily
EA [auth g]IPR032454Histone H2A, C-terminal domainDomain
EA [auth g]IPR032458Histone H2A conserved siteConserved Site
EA [auth g]IPR007125Core Histone H2A/H2B/H3 domainDomain
AA [auth a],
CA [auth e]		IPR009072Histone-foldHomologous Superfamily
AA [auth a],
CA [auth e]		IPR000164Histone H3/CENP-AFamily
AA [auth a],
CA [auth e]		IPR007125Core Histone H2A/H2B/H3 domainDomain
IPR041976Spt5, KOW domain repeat 3Domain
IPR041980Spt5, KOW domain repeat 6, metazoaDomain
IPR039385NGN domain, eukaryoticDomain
IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
IPR022581Spt5 transcription elongation factor, N-terminalDomain
IPR024945Spt5 C-terminal domainDomain
IPR006645NusG-like, N-terminalDomain
IPR041975Spt5, KOW domain repeat 2Domain
IPR039659Transcription elongation factor SPT5Family
IPR036735NusG, N-terminal domain superfamilyHomologous Superfamily
IPR008991Translation protein SH3-like domain superfamilyHomologous Superfamily
IPR041973Spt5, KOW domain repeat 1Domain
IPR005100NGN domainDomain
IPR041977Spt5, KOW domain repeat 4Domain
IPR017071Transcription elongation factor Spt5, eukaryoteFamily
IPR005824KOWDomain
IPR041978Spt5, KOW domain repeat 5Domain
IPR019775WD40 repeat, conserved siteConserved Site
IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
IPR051510Superkiller complex protein 8Family
IPR020472PAC1/LIS1-like, WD-40 repeatRepeat
IPR001680WD40 repeatRepeat
IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
IPR007149Leo1-like proteinFamily
IPR036128Plus3-like superfamilyHomologous Superfamily
IPR004343Plus-3 domainDomain
IPR042066Spt6, Death-like domainHomologous Superfamily
IPR028231Transcription elongation factor Spt6, YqgF domainDomain
IPR037027YqgF/RNase H-like domain superfamilyHomologous Superfamily
IPR036860SH2 domain superfamilyHomologous Superfamily
IPR000980SH2 domainDomain
IPR006641YqgF/RNase H-like domainDomain
IPR041692HHH domain 9Domain
IPR010994RuvA domain 2-likeHomologous Superfamily
IPR023319Tex-like protein, HTH domain superfamilyHomologous Superfamily
IPR012337Ribonuclease H-like superfamilyHomologous Superfamily
IPR017072Transcription elongation factor Spt6Family
IPR035420Spt6, SH2 domainDomain
IPR032706Transcription elongation factor Spt6, helix-hairpin-helix motifDomain
IPR003029S1 domainDomain
IPR023323Tex-like domain superfamilyHomologous Superfamily
IPR055179Tex-like, central regionDomain
IPR028088Helix-turn-helix DNA-binding domain of Spt6Domain
IPR035019Spt6, SH2 domain, N terminusDomain
IPR035018Spt6, SH2 domain, C terminusDomain
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR028083Spt6 acidic, N-terminal domainDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
Pharos:  Q96ST2
Pharos:  Q6PD62
Pharos:  P23193
Pharos:  Q8N7H5
Pharos:  Q6P1J9
Pharos:  P63272
GA [auth l]Pharos:  Q9BYW2
HA [auth x]Pharos:  Q9Y5B9
IA [auth y]Pharos:  Q08945
Pharos:  O00267
Pharos:  Q9GZS3
Pharos:  Q8WVC0
Pharos:  Q92541
Pharos:  Q7KZ85

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
SEP Parent Component: SER

RESID:  AA0037

PSI-MOD :  O-phospho-L-serine MOD:00046
TPO Parent Component: THR

RESID:  AA0037 , AA0038

PSI-MOD :  O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047
TPO Parent Component: THR

RESID:  AA0037 , AA0038 , AA0038

PSI-MOD :  O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047 , O-phospho-L-threonine MOD:00047