Research workbench
Cryo-EM structure of E. COLI RNA polymerase elongation complex bound to greb transcription factor
Analyse Cryo-EM structure of E. COLI RNA polymerase elongation complex bound to greb… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RI7
- Type
- protein + DNA + RNA
- Length
- 3,583 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-template DNA; Template DNA; Transcription elongation factor greb; DNA-directed RNA…
- EC
- 2.7.7.6
- UniProt
- C3SQ22, P0A7Z4, P0A8V2, P0A8T7, P0A800
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 9 distinct chains · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Non-template DNA | dna | 22 | — | — |
| T | Template DNA | dna | 32 | — | — |
| F, G | Transcription elongation factor greb | protein | 156 | 39% helix, 21% strand | C3SQ22 |
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 23% helix, 32% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 229 | 23% helix, 35% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1319 | 31% helix, 20% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1358 | 38% helix, 15% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 73 | 60% helix, 0% strand | P0A800 |
| R | RNA | rna | 10 | — | — |
Ligands and binding sites
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 | 788 | 0.87 | 0.91 | 99 | empty |
| 2 | 998 | 0.87 | 0.88 | 139 | empty |
| 3 | 1138 | 0.86 | 0.88 | 110 | empty |
| 4 | 509 | 0.82 | 0.88 | 55 | empty |
| 5 | 1115 | 0.81 | 0.82 | 108 | empty |
Interfaces
21 interfaces between chains.
- C–D · 8433 Ų buried · 92 hydrogen bonds · protein-protein
- F–D · 2836 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1999 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1998 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 1312 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6RI7 · Cryo-EM structure of E. coli RNA polymerase elongation complex bound to GreB… · the same entry in another collection · chain G against G, TM-score 1.00
- P0A8V2 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V2) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 C3SQ22
- Every structure of UniProt P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Elsewhere: RCSB PDB 6RI7 · PDBe 6RI7 · UniProt C3SQ22 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800
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