6TED
Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers allosteric elongation activation by RTF1
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
D | SCOP2B Superfamily | HRDC-like | 8101241 | 3000132 | SCOP2B (2022-06-29) |
F | SCOP2B Superfamily | RPB6/omega subunit-like | 8106082 | 3000189 | SCOP2B (2022-06-29) |
J | SCOP2 Family | RNA polymerase subunit RPB10 | 8101286 | 4000742 | SCOP2 (2022-06-29) |
J | SCOP2 Superfamily | RNA polymerase subunit RPB10 | 8101287 | 3001213 | SCOP2 (2022-06-29) |
K | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8080728 | 3001655 | SCOP2B (2022-06-29) |
L | SCOP2B Superfamily | RNA polymerase subunits | 8103068 | 3001823 | SCOP2B (2022-06-29) |
Q [auth R] | SCOP2B Superfamily | Plus3-like | 8033751 | 3000248 | SCOP2B (2022-06-29) |
X [auth Z] | SCOP2B Superfamily | Translation proteins SH3-like KOW motif containing domain | 8039849 | 3000334 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
B | RNA_pol_Rpb2_6_3rd_2 | e6tedB6 | A: beta barrels | X: cradle loop barrel | H: RIFT-related | T: double psi | F: RNA_pol_Rpb2_6_3rd_2 | ECOD (1.6) |
B | RNA_pol_Rpb2_6_2nd_1 | e6tedB3 | A: a+b complex topology | X: alpha/beta-Hammerhead/Barrel-sandwich hybrid | H: alpha/beta-Hammerhead/Barrel-sandwich hybrid | T: Single hybrid motif | F: RNA_pol_Rpb2_6_2nd_1 | ECOD (1.6) |
B | RNA_pol_Rpb2_3 | e6tedB7 | A: a+b complex topology | X: 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-polymerase | F: RNA_pol_Rpb2_3 | ECOD (1.6) |
B | RNA_pol_Rpb2_1 | e6tedB5 | A: a+b complex topology | X: 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-polymerase | F: RNA_pol_Rpb2_1 | ECOD (1.6) |
B | RNA_pol_Rpb2_45_1 | e6tedB1 | A: a+b complex topology | X: 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-polymerase | F: RNA_pol_Rpb2_45_1 | ECOD (1.6) |
B | RNA_pol_Rpb2_7 | e6tedB4 | A: a+b complex topology | X: 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-polymerase | F: RNA_pol_Rpb2_7 | ECOD (1.6) |
B | RNA_pol_Rpb2_4 | e6tedB2 | A: a+b complex topology | X: 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 subunit | F: RNA_pol_Rpb2_4 | ECOD (1.6) |
C | RNA_pol_L_1 | e6tedC1 | A: a+b two layers | X: DCoH-like | H: RBP11-like subunits of RNA polymerase (From Topology) | T: RBP11-like subunits of RNA polymerase | F: RNA_pol_L_1 | ECOD (1.6) |
C | RNA_pol_A_bac_1 | e6tedC2 | A: a+b complex topology | X: Ribosomal protein TL5/L25 C-terminal domain-like | H: Insert subdomain of RNA polymerase alpha subunit (From Topology) | T: Insert subdomain of RNA polymerase alpha subunit | F: RNA_pol_A_bac_1 | ECOD (1.6) |
D | RNA_pol_Rpb4 | e6tedD1 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: RNA_pol_Rpb4 | ECOD (1.6) |
E | RNA_pol_Rpb5_C | e6tedE1 | A: a+b two layers | X: RPB5-like RNA polymerase subunit (From Topology) | H: RPB5-like RNA polymerase subunit (From Topology) | T: RPB5-like RNA polymerase subunit | F: RNA_pol_Rpb5_C | ECOD (1.6) |
E | RNA_pol_Rpb5_N | e6tedE2 | A: a/b three-layered sandwiches | X: Restriction endonuclease-like | H: Eukaryotic RPB5 N-terminal domain (From Topology) | T: Eukaryotic RPB5 N-terminal domain | F: RNA_pol_Rpb5_N | ECOD (1.6) |
F | RNA_pol_Rpb6_1 | e6tedF1 | A: alpha arrays | X: RPB6/omega subunit-like (From Homology) | H: RPB6/omega subunit-like | T: RPB6 | F: RNA_pol_Rpb6_1 | ECOD (1.6) |
G | S1_1 | e6tedG1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: S1_1 | ECOD (1.6) |
G | SHS2_Rpb7-N | e6tedG2 | A: a+b two layers | X: Dodecin subunit-like | H: Flavin-binding protein dodecin-like (From Topology) | T: Flavin-binding protein dodecin-like | F: SHS2_Rpb7-N | ECOD (1.6) |
H | RNA_pol_Rpb8 | e6tedH1 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: RNA_pol_Rpb8 | ECOD (1.6) |
I | RNA_POL_M_15KD | e6tedI1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: RNA_POL_M_15KD | ECOD (1.6) |
I | TFIIS_C | e6tedI2 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: TFIIS_C | ECOD (1.6) |
J | RNA_pol_N | e6tedJ1 | A: alpha arrays | X: HTH | H: RPB10 (From Topology) | T: RPB10 | F: RNA_pol_N | ECOD (1.6) |
K | RNA_pol_L_2 | e6tedK1 | A: a+b two layers | X: DCoH-like | H: RBP11-like subunits of RNA polymerase (From Topology) | T: RBP11-like subunits of RNA polymerase | F: RNA_pol_L_2 | ECOD (1.6) |
L | DNA_RNApol_7kD | e6tedL1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: DNA_RNApol_7kD | ECOD (1.6) |
M | S1_1 | e6tedM3 | A: beta barrels | X: OB-fold | H: Nucleic acid-binding proteins (From Topology) | T: Nucleic acid-binding proteins | F: S1_1 | ECOD (1.6) |
M | HTH_44 | e6tedM1 | A: alpha arrays | X: HTH | H: Tex N-terminal domain (From Topology) | T: Tex N-terminal domain | F: HTH_44 | ECOD (1.6) |
M | DLD | e6tedM7 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: DLD | ECOD (1.6) |
M | HHH_7 | e6tedM4 | A: alpha arrays | X: HhH/H2TH | H: SAM/DNA-glycosylase | T: SAM domain-like | F: HHH_7 | ECOD (1.6) |
M | UNK_F_TYPE | e6tedM6 | A: alpha bundles | X: immunoglobulin/albumin-binding domain-like | H: Tex bundle domain-like (From Topology) | T: Tex bundle domain-like | F: UNK_F_TYPE | ECOD (1.6) |
M | Tex_N_3rd | e6tedM9 | A: alpha complex topology | X: Tex N-terminal region-like (From Topology) | H: Tex N-terminal region-like (From Topology) | T: Tex N-terminal region-like | F: Tex_N_3rd | ECOD (1.6) |
M | SH2_2_C | e6tedM2 | A: a+b two layers | X: SH2 (From Topology) | H: SH2 (From Topology) | T: SH2 | F: SH2_2_C | ECOD (1.6) |
M | SH2_2_N | e6tedM5 | A: a+b two layers | X: SH2 (From Topology) | H: SH2 (From Topology) | T: SH2 | F: SH2_2_N | ECOD (1.6) |
M | Tex_YqgF | e6tedM8 | A: mixed a+b and a/b | X: Ribonuclease H-like | H: Ribonuclease H-like (From Topology) | T: Ribonuclease H-like | F: Tex_YqgF | ECOD (1.6) |
U [auth W] | ANAPC4_WD40_7 | e6tedW1 | A: beta duplicates or obligate multimers | X: beta-propeller-like | H: beta-propeller | T: 7-bladed | F: ANAPC4_WD40_7 | ECOD (1.6) |
W [auth Y] | Spt4 | e6tedY1 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: Spt4 | ECOD (1.6) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF04561 | RNA polymerase Rpb2, domain 2 (RNA_pol_Rpb2_2) | RNA polymerase Rpb2, domain 2 | 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 po ... | Domain | |
PF04560 | RNA polymerase Rpb2, domain 7 (RNA_pol_Rpb2_7) | RNA polymerase Rpb2, domain 7 | 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 p ... | Domain | |
PF04565 | RNA polymerase Rpb2, domain 3 (RNA_pol_Rpb2_3) | RNA polymerase Rpb2, domain 3 | 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 ... | Domain | |
PF04566 | RNA polymerase Rpb2, domain 4 (RNA_pol_Rpb2_4) | RNA polymerase Rpb2, domain 4 | 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 ... | Domain | |
PF04563 | RNA polymerase beta subunit (RNA_pol_Rpb2_1) | RNA polymerase beta subunit | - | Family | |
PF00562 | RNA polymerase Rpb2, domain 6 (RNA_pol_Rpb2_6) | RNA polymerase Rpb2, domain 6 | 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 ... | Domain | |
PF04567 | RNA polymerase Rpb2, domain 5 (RNA_pol_Rpb2_5) | RNA polymerase Rpb2, domain 5 | 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 ... | Domain | |
PF01193 | RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L) | RNA polymerase Rpb3/Rpb11 dimerisation domain | 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 do ... | Domain | |
PF01000 | RNA polymerase Rpb3/RpoA insert domain (RNA_pol_A_bac) | RNA polymerase Rpb3/RpoA insert domain | Members of this family include: alpha subunit from eubacteria alpha subunits from chloroplasts Rpb3 subunits from eukaryotes RpoD subunits from archaeal | Domain | |
PF03874 | RNA polymerase Rpb4 (RNA_pol_Rpb4) | RNA polymerase Rpb4 | - | Family | |
PF01191 | RNA polymerase Rpb5, C-terminal domain (RNA_pol_Rpb5_C) | RNA polymerase Rpb5, C-terminal domain | The assembly domain of Rpb5 [1]. The archaeal equivalent to this domain is subunit H. Subunit H lacks the N-terminal domain. | Domain | |
PF03871 | RNA polymerase Rpb5, N-terminal domain (RNA_pol_Rpb5_N) | RNA polymerase Rpb5, N-terminal domain | 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 p ... | Domain | |
PF01192 | RNA polymerase Rpb6 (RNA_pol_Rpb6) | RNA polymerase Rpb6 | - | Family | |
PF03870 | RNA polymerase Rpb8 (RNA_pol_Rpb8) | RNA polymerase Rpb8 | - | Family | |
PF02150 | RNA polymerases M/15 Kd subunit (RNA_POL_M_15KD) | RNA polymerases M/15 Kd subunit | - | Domain | |
PF01096 | Transcription factor S-II (TFIIS) (TFIIS_C) | Transcription factor S-II (TFIIS) | - | Domain | |
PF01194 | RNA polymerases N / 8 kDa subunit (RNA_pol_N) | RNA polymerases N / 8 kDa subunit | - | Domain | |
PF13656 | RNA polymerase Rpb3/Rpb11 dimerisation domain (RNA_pol_L_2) | RNA polymerase Rpb3/Rpb11 dimerisation domain | 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 do ... | Domain | |
PF03604 | DNA directed RNA polymerase, 7 kDa subunit (DNA_RNApol_7kD) | DNA directed RNA polymerase, 7 kDa subunit | - | Domain | |
PF14639 | Holliday-junction resolvase-like of SPT6 (YqgF) | Holliday-junction resolvase-like of SPT6 | The 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 | |
PF17674 | HHH domain (HHH_9) | HHH domain | - | Domain | |
PF14641 | Helix-turn-helix DNA-binding domain of SPT6 (HTH_44) | Helix-turn-helix DNA-binding domain of SPT6 | This helix-turn-helix represents the first of two DNA-binding domains on the SPT6 proteins. | Domain | |
PF22706 | Tex central region-like (Tex_central_region) | Tex central region-like | 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 ... | Domain | |
PF14635 | Helix-hairpin-helix motif (HHH_7) | Helix-hairpin-helix motif | - | Domain | |
P [auth Q] | PF13181 | Tetratricopeptide repeat (TPR_8) | Tetratricopeptide repeat | - | Repeat |
P [auth Q] | PF13374 | Tetratricopeptide repeat (TPR_10) | Tetratricopeptide repeat | - | Repeat |
Q [auth R] | PF03126 | Plus-3 domain (Plus-3) | Plus-3 domain | 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 ... | Domain |
S [auth U] | PF04004 | Leo1-like protein (Leo1) | Leo1-like protein | - | Family |
T [auth V] | PF03985 | Paf1 (Paf1) | Paf1 | - | Family |
U [auth W] | PF00400 | WD domain, G-beta repeat (WD40) | WD domain, G-beta repeat | - | Repeat |
W [auth Y] | PF06093 | Spt4/RpoE2 zinc finger (Spt4) | Spt4/RpoE2 zinc finger | 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 ... | Domain |
X [auth Z] | PF03439 | Early transcription elongation factor of RNA pol II, NGN section (Spt5-NGN) | Early transcription elongation factor of RNA pol II, NGN section | - | Family |
X [auth Z] | PF00467 | KOW motif (KOW) | KOW motif | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Pharos: Disease Associations Pharos Homepage Annotation
Protein Modification Annotation
Modified Residue(s) | ||
---|---|---|
Chain | Residue(s) | Description |
SEP | Parent Component: SER :  AA0037 :  O-phospho-L-serine MOD:00046 | |
TPO | Parent Component: THR :  AA0037 , AA0038 :  O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047 | |
X [auth Z] | TPO | Parent Component: THR :  AA0037 , AA0038 , AA0038 :  O-phospho-L-serine MOD:00046 , O-phospho-L-threonine MOD:00047 , O-phospho-L-threonine MOD:00047 |