Research workbench
Cryo-EM structure of E. COLI RNA polymerase backtracked elongation complex bound to greb transcription factor
Analyse Cryo-EM structure of E. COLI RNA polymerase backtracked elongation complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RIN
- Type
- protein + DNA + RNA
- Length
- 3,422 residues
- Chains
- 9
- 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 0.86
Structure
electron microscopy · 9 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Non-template DNA | dna | 19 | — | — |
| T | Template DNA | dna | 27 | — | — |
| F | Transcription elongation factor greb | protein | 156 | 37% helix, 19% strand | C3SQ22 |
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 24% helix, 35% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 229 | 23% helix, 33% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1319 | 30% helix, 18% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1358 | 36% helix, 15% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 73 | 58% helix, 0% strand | P0A800 |
| R | RNA | rna | 13 | — | — |
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 | 877 | 0.86 | 0.89 | 96 | empty |
| 2 | 889 | 0.85 | 0.88 | 113 | empty |
| 3 | 731 | 0.83 | 0.87 | 71 | empty |
| 4 | 1082 | 0.81 | 0.83 | 87 | empty |
| 5 | 1172 | 0.81 | 0.82 | 99 | empty |
Interfaces
19 interfaces between chains.
- C–D · 8248 Ų buried · 74 hydrogen bonds · protein-protein
- F–D · 2705 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 1929 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1827 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1277 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6RIN · Cryo-EM structure of E. coli RNA polymerase backtracked elongation complex bound to GreB… · the same entry in another collection · chain R against R, 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 0.98
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 6RIN · PDBe 6RIN · UniProt C3SQ22 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800
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