Research workbench
Structure of paused transcription complex pol II-dsif-nelf
Analyse Structure of paused transcription complex pol II-dsif-nelf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GML
- Type
- protein + DNA + RNA
- Length
- 5,774 residues
- Chains
- 21
- 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
- I3LGP4, I3LCH3, I3LSI7, F1SKN8, I3LCB2, P60899, F1RKE4, I3LN51, Q9H3P2, Q8WX92, Q8IXH7, P18615, P63272, O00267, A0A287ADR4, I3LJZ9
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 21 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit (EC 2.7.7.6) | protein | 1407 | 39% helix, 14% strand | — |
| B | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1116 | 27% helix, 25% strand | I3LGP4 |
| C | RNA polymerase II subunit C | protein | 258 | 24% helix, 27% strand | I3LCH3 |
| E | RNA polymerase II subunit E | protein | 209 | 37% helix, 17% strand | I3LSI7 |
| F | RNA polymerase II subunit F | protein | 82 | 32% helix, 16% strand | F1SKN8 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 148 | 2% helix, 48% strand | I3LCB2 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 117 | 8% helix, 26% strand | P60899 |
| J | Uncharacterized protein | protein | 67 | 42% helix, 4% strand | — |
| K | Uncharacterized protein | protein | 115 | 39% helix, 25% strand | F1RKE4 |
| L | Uncharacterized protein | protein | 46 | 0% helix, 20% strand | I3LN51 |
| N | Non-template DNA | dna | 36 | — | — |
| P | Tar RNA | rna | 17 | — | — |
| T | Template DNA | dna | 45 | — | — |
| U | Negative elongation factor a | protein | 183 | 54% helix, 1% strand | Q9H3P2 |
| V | Negative elongation factor B,NEGATIVE elongation factor B | protein | 483 | 66% helix, 0% strand | Q8WX92 |
| W | Negative elongation factor C/D | protein | 538 | 65% helix, 1% strand | Q8IXH7 |
| X | Negative elongation factor E,NEGATIVE elongation factor E | protein | 22 | 64% helix, 0% strand | P18615 |
| Y | Transcription elongation factor SPT4 | protein | 116 | 30% helix, 23% strand | P63272 |
| Z | Transcription elongation factor SPT5 | protein | 470 | 10% helix, 36% strand | O00267 |
| D | RNA polymerase II subunit D | protein | 128 | 60% helix, 3% strand | A0A287ADR4 |
| G | RNA polymerase II subunit G | protein | 171 | 10% helix, 51% strand | I3LJZ9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 9 copies · chains A, B, C, Z, 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 | 733 | 0.86 | 0.90 | 81 | empty |
| 2 | 1183 | 0.86 | 0.87 | 117 | empty |
| 3 | 713 | 0.81 | 0.85 | 94 | empty |
| 4 | 192 | 0.80 | 0.94 | 39 | empty |
| 5 | 342 | 0.80 | 0.90 | 48 | empty |
Interfaces
53 interfaces between chains.
- A–B · 8937 Ų buried · 116 hydrogen bonds · protein-protein
- U–W · 4273 Ų buried · 40 hydrogen bonds · protein-protein
- A–E · 2405 Ų buried · 32 hydrogen bonds · protein-protein
- C–K · 2328 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 2258 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- P63272 · AlphaFold monomer V2.0 prediction for transcription elongation factor SPT4 (P63272) · a predicted model of the same protein · chain Y against A, TM-score 0.98
- Q8IXH7 · AlphaFold monomer V2.0 prediction for negative elongation factor C/D (Q8IXH7) · a predicted model of the same protein · chain W against A, TM-score 0.92
- Q9H3P2 · AlphaFold monomer V2.0 prediction for negative elongation factor a (Q9H3P2) · a predicted model of the same protein · chain U against A, TM-score 0.92
- Q8WX92 · AlphaFold monomer V2.0 prediction for negative elongation factor B (Q8WX92) · a predicted model of the same protein · chain V against A, TM-score 0.86
- P60899 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase II subunit RPB9 (P60899) · a predicted model of the same protein · chain I against A, TM-score 0.86
- P18615 · AlphaFold monomer V2.0 prediction for negative elongation factor E (P18615) · a predicted model of the same protein · chain X against A, TM-score 0.62
- O00267 · AlphaFold monomer V2.0 prediction for transcription elongation factor SPT5 (O00267) · a predicted model of the same protein · chain Z against A, TM-score 0.54
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 I3LGP4
- Every structure of UniProt I3LCH3
- Every structure of UniProt I3LSI7
- Every structure of UniProt F1SKN8
- Every structure of UniProt I3LCB2
- Every structure of UniProt P60899
- Every structure of UniProt F1RKE4
- Every structure of UniProt I3LN51
- Every structure of UniProt Q9H3P2
- Every structure of UniProt Q8WX92
- Every structure of UniProt Q8IXH7
- Every structure of UniProt P18615
- Every structure of UniProt P63272
- Every structure of UniProt O00267
- Every structure of UniProt A0A287ADR4
- Every structure of UniProt I3LJZ9
- Elsewhere: RCSB PDB 6GML · PDBe 6GML · UniProt I3LGP4 · UniProt I3LCH3 · UniProt I3LSI7 · UniProt F1SKN8 · UniProt I3LCB2 · UniProt P60899 · UniProt F1RKE4 · UniProt I3LN51 · UniProt Q9H3P2 · UniProt Q8WX92 · UniProt Q8IXH7 · UniProt P18615 · UniProt P63272 · UniProt O00267 · UniProt A0A287ADR4 · UniProt I3LJZ9
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