8A3Y
Structure of mammalian Pol II-DSIF-SPT6-PAF1-TFIIS-hexasome elongation complex
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) |
J | SCOP2B Superfamily | RNA polymerase subunit RPB10 | 8101287 | 3001213 | SCOP2B (2022-06-29) |
K | SCOP2B Superfamily | RBP11-like subunits of RNA polymerase | 8080728 | 3001655 | 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) |
CA [auth e] | SCOP2B Superfamily | Core histone-like | 8041272 | 3001387 | SCOP2B (2022-06-29) |
Y [auth a] | SCOP2B Superfamily | Core histone-like | 8041272 | 3001387 | SCOP2B (2022-06-29) |
DA [auth f] | SCOP2B Superfamily | Core histone-like | 8042439 | 3001387 | SCOP2B (2022-06-29) |
Z [auth b] | SCOP2B Superfamily | Core histone-like | 8042439 | 3001387 | SCOP2B (2022-06-29) |
AA [auth c] | SCOP2B Superfamily | Core histone-like | 8067126 | 3001387 | SCOP2B (2022-06-29) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF00623 | RNA polymerase Rpb1, domain 2 (RNA_pol_Rpb1_2) | RNA polymerase Rpb1, 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). This domain, domain 2, contains the active site ... | Domain | |
PF04990 | RNA polymerase Rpb1, domain 7 (RNA_pol_Rpb1_7) | RNA polymerase Rpb1, 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). This domain, domain 7, represents a mobile modu ... | Domain | |
PF05000 | RNA polymerase Rpb1, domain 4 (RNA_pol_Rpb1_4) | RNA polymerase Rpb1, 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). This domain, domain 4, represents the funnel do ... | Domain | |
PF04983 | RNA polymerase Rpb1, domain 3 (RNA_pol_Rpb1_3) | RNA polymerase Rpb1, 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). This domain, domain 3, represents the pore doma ... | Domain | |
PF04992 | RNA polymerase Rpb1, domain 6 (RNA_pol_Rpb1_6) | RNA polymerase Rpb1, 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, domain 6, represents a mobile modu ... | Domain | |
PF04998 | RNA polymerase Rpb1, domain 5 (RNA_pol_Rpb1_5) | RNA polymerase Rpb1, 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). This domain, domain 5, represents the discontin ... | Domain | |
PF04997 | RNA polymerase Rpb1, domain 1 (RNA_pol_Rpb1_1) | RNA polymerase Rpb1, domain 1 | 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 do ... | Domain | |
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 | |
PF15511 | Centromere kinetochore component CENP-T histone fold (CENP-T_C) | Centromere kinetochore component CENP-T histone fold | 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 asso ... | Domain | |
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 | |
PF03874 | RNA polymerase Rpb4 (RNA_pol_Rpb4) | RNA polymerase Rpb4 | - | Family | |
PF00125 | Core histone H2A/H2B/H3/H4 (Histone) | Core histone H2A/H2B/H3/H4 | - | Domain | |
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 | |
PF03876 | SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 (SHS2_Rpb7-N) | SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 | 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 leas ... | Domain | |
PF00575 | S1 RNA binding domain (S1) | S1 RNA binding domain | The 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 | |
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 | |
P [auth Q], S [auth U] | PF13181 | Tetratricopeptide repeat (TPR_8) | Tetratricopeptide repeat | - | Repeat |
P [auth Q], S [auth U] | PF13374 | Tetratricopeptide repeat (TPR_10) | Tetratricopeptide repeat | - | Repeat |
P [auth Q], S [auth U] | PF04004 | Leo1-like protein (Leo1) | Leo1-like protein | - | Family |
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 |
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 |
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 | |
PF16211 | C-terminus of histone H2A (Histone_H2A_C) | C-terminus of histone H2A | - | Family | |
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 | |
PF00125 | Core histone H2A/H2B/H3/H4 (Histone) | Core histone H2A/H2B/H3/H4 | - | Domain |
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 |