Research workbench
Cryo-EM structure of bacterial RNA polymerase-SIGMA54 holoenzyme initial transcribing complex
Analyse Cryo-EM structure of bacterial RNA polymerase-SIGMA54 holoenzyme initial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GFW
- Type
- protein + DNA + RNA
- Length
- 3,698 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, P0A800, A0A0J4U551, A0A2A5PML4
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 9 distinct chains · 32% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 22% helix, 26% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 235 | 22% helix, 33% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 30% helix, 20% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1345 | 32% helix, 9% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 74 | 62% helix, 0% strand | P0A800 |
| F | Nifh promoter template DNA | dna | 50 | — | — |
| G | Nifh promoter non-template DNA | dna | 50 | — | — |
| M | RNA polymerase sigma-54 factor (EC 2.7.7.6) | protein | 366 | 47% helix, 1% strand | A0A0J4U551, A0A2A5PML4 |
| R | De novo synthesized RNA | rna | 4 | — | — |
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 | 855 | 0.83 | 0.85 | 94 | empty |
| 2 | 1125 | 0.83 | 0.84 | 93 | empty |
| 3 | 1127 | 0.82 | 0.83 | 103 | empty |
| 4 | 569 | 0.82 | 0.87 | 79 | empty |
| 5 | 1002 | 0.81 | 0.83 | 97 | empty |
Interfaces
21 interfaces between chains.
- C–D · 7595 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 2137 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 1758 Ų buried · 181 hydrogen bonds · nucleic-nucleic
- A–C · 1488 Ų buried · 14 hydrogen bonds · protein-protein
- C–M · 1249 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6GFW · Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme initial transcribing… · 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 0.95
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 P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Every structure of UniProt A0A0J4U551
- Every structure of UniProt A0A2A5PML4
- Elsewhere: RCSB PDB 6GFW · PDBe 6GFW · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt A0A0J4U551 · UniProt A0A2A5PML4
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