Research workbench
Cryo-EM structure of bacterial RNA polymerase-SIGMA54 holoenzyme transcription open complex
Analyse Cryo-EM structure of bacterial RNA polymerase-SIGMA54 holoenzyme transcription… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GH5
- Type
- protein + DNA
- Length
- 3,735 residues
- Chains
- 8
- 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
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 8 distinct chains · 32% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 309 | 25% helix, 25% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 235 | 20% helix, 29% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 31% helix, 18% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1345 | 33% helix, 9% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 75 | 63% helix, 0% strand | P0A800 |
| M | RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 factor, RNA polymerase sigma-54 factor (EC 2.7.7.6) | protein | 338 | 45% helix, 3% strand | A0A0J4U551 |
| F | Nifh promoter template DNA | dna | 46 | — | — |
| G | Nifh promoter non-template DNA | dna | 46 | — | — |
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 | 945 | 0.83 | 0.85 | 79 | empty |
| 2 | 878 | 0.83 | 0.85 | 68 | empty |
| 3 | 847 | 0.82 | 0.85 | 81 | empty |
| 4 | 575 | 0.82 | 0.87 | 64 | empty |
| 5 | 1048 | 0.80 | 0.81 | 99 | empty |
Interfaces
18 interfaces between chains.
- C–D · 7673 Ų buried · 85 hydrogen bonds · protein-protein
- A–B · 2141 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1729 Ų buried · 18 hydrogen bonds · protein-protein
- F–G · 1603 Ų buried · 153 hydrogen bonds · nucleic-nucleic
- C–M · 1363 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6GH5 · Cryo-EM structure of bacterial RNA polymerase-sigma54 holoenzyme transcription open… · 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 0.96
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
- Elsewhere: RCSB PDB 6GH5 · PDBe 6GH5 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt A0A0J4U551
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