Research workbench
Structure of complete, activated transcription complex pol II-dsif- paf-SPT6 uncovers allosteric elongation activation by RTF1
Analyse Structure of complete, activated transcription complex pol II-dsif- paf-SPT6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TED
- Type
- protein + DNA + RNA
- Length
- 7,463 residues
- Chains
- 24
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase subunit beta; RNA…
- EC
- 2.7.7.6
- UniProt
- A0A480RVL6, I3LGP4, I3LCH3, A0A287ADR4, I3LSI7, F1SKN8, I3LJZ9, I3LCB2, P60899, A0A287B432, F1RKE4, I3LN51, Q7KZ85, Q6PD62, Q92541, Q8WVC0, Q8N7H5, Q9GZS3, Q6P1J9, P63272, O00267
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 24 distinct chains · 32% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 1426 | 38% helix, 12% strand | A0A480RVL6 |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1122 | 27% helix, 22% strand | I3LGP4 |
| C | RNA polymerase II subunit C | protein | 258 | 21% helix, 26% strand | I3LCH3 |
| D | RNA polymerase II subunit D | protein | 126 | 59% helix, 2% strand | A0A287ADR4 |
| E | RNA polymerase II subunit E | protein | 209 | 35% helix, 18% strand | I3LSI7 |
| F | RNA polymerase II subunit F | protein | 78 | 33% helix, 17% strand | F1SKN8 |
| G | RNA polymerase II subunit G | protein | 171 | 8% helix, 37% strand | I3LJZ9 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 149 | 2% helix, 40% strand | I3LCB2 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 116 | 7% helix, 26% strand | P60899 |
| J | Uncharacterized protein | protein | 66 | 50% helix, 5% strand | A0A287B432 |
| K | Uncharacterized protein | protein | 115 | 39% helix, 22% strand | F1RKE4 |
| L | Uncharacterized protein | protein | 47 | 0% helix, 26% strand | I3LN51 |
| M | Transcription elongation factor SPT6 | protein | 1002 | 40% helix, 11% strand | Q7KZ85 |
| N | DNA (37-mer) | dna | 37 | — | — |
| P | RNA (5'- R(P*UP*AP*AP*CP*CP*GP*GP*AP*GP*AP*GP*GP*GP*AP*AP*CP*CP*CP*AP*CP*U)- 3') | rna | 21 | — | — |
| Q | RNA polymerase-associated protein CTR9 homolog | protein | 890 | 65% helix, 1% strand | Q6PD62 |
| R | RNA polymerase-associated protein RTF1 homolog | protein | 244 | 49% helix, 16% strand | Q92541 |
| T | Template DNA | dna | 48 | — | — |
| U | RNA polymerase-associated protein LEO1 | protein | 125 | 6% helix, 25% strand | Q8WVC0 |
| V | RNA polymerase II-associated factor 1 homolog | protein | 244 | 11% helix, 10% strand | Q8N7H5 |
| W | Wd repeat-containing protein 61 | protein | 300 | 0% helix, 48% strand | Q9GZS3 |
| X | Parafibromin | protein | 43 | 49% helix, 2% strand | Q6P1J9 |
| Y | Transcription elongation factor SPT4 | protein | 116 | 20% helix, 17% strand | P63272 |
| Z | Transcription elongation factor SPT5 | protein | 510 | 9% helix, 28% strand | O00267 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, I, J, L, Y
- MG · Magnesium ion · metal · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.89 | 0.90 | 119 | empty |
| 2 | 1051 | 0.87 | 0.89 | 119 | empty |
| 3 | 1053 | 0.86 | 0.87 | 108 | empty |
| 4 | 1148 | 0.84 | 0.85 | 100 | empty |
| 5 | 542 | 0.83 | 0.89 | 56 | empty |
Interfaces
72 interfaces between chains.
- A–B · 8799 Ų buried · 97 hydrogen bonds · protein-protein
- Q–V · 5410 Ų buried · 41 hydrogen bonds · protein-protein
- A–E · 2314 Ų buried · 28 hydrogen bonds · protein-protein
- U–V · 2313 Ų buried · 26 hydrogen bonds · protein-protein
- C–K · 2206 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 modified (phosphorylation).
Compared structures
- 6TED · Structure of complete, activated transcription complex Pol II-DSIF-PAF-SPT6 uncovers… · the same entry in another collection · chain J against J, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A480RVL6
- Every structure of UniProt I3LGP4
- Every structure of UniProt I3LCH3
- Every structure of UniProt A0A287ADR4
- Every structure of UniProt I3LSI7
- Every structure of UniProt F1SKN8
- Every structure of UniProt I3LJZ9
- Every structure of UniProt I3LCB2
- Every structure of UniProt P60899
- Every structure of UniProt A0A287B432
- Every structure of UniProt F1RKE4
- Every structure of UniProt I3LN51
- Every structure of UniProt Q7KZ85
- Every structure of UniProt Q6PD62
- Every structure of UniProt Q92541
- Every structure of UniProt Q8WVC0
- Every structure of UniProt Q8N7H5
- Every structure of UniProt Q9GZS3
- Every structure of UniProt Q6P1J9
- Every structure of UniProt P63272
- Every structure of UniProt O00267
- Elsewhere: RCSB PDB 6TED · PDBe 6TED · UniProt A0A480RVL6 · UniProt I3LGP4 · UniProt I3LCH3 · UniProt A0A287ADR4 · UniProt I3LSI7 · UniProt F1SKN8 · UniProt I3LJZ9 · UniProt I3LCB2 · UniProt P60899 · UniProt A0A287B432 · UniProt F1RKE4 · UniProt I3LN51 · UniProt Q7KZ85 · UniProt Q6PD62 · UniProt Q92541 · UniProt Q8WVC0 · UniProt Q8N7H5 · UniProt Q9GZS3 · UniProt Q6P1J9 · UniProt P63272 · UniProt O00267
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