MolNFT v1 · #128518 · protein + DNA
Cryo-EM structure of RNA polymerase-SIGMA54 holo enzyme with promoter DNA closed complex
5NSR · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of RNA polymerase-SIGMA54 holo enzyme with promoter DNA closed complex”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #128518 on GenesisL1: 3D…
- PDB
- 5NSR
- Type
- protein + DNA
- Length
- 3,631 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 0.84
Structure
electron microscopy · 8 distinct chains · 32% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 23% helix, 24% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 223 | 18% helix, 29% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 30% helix, 16% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1320 | 35% helix, 7% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 74 | 59% 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,RNA polymerase sigma-54 FACTOR,RNA polymerase sigma-54 factor | protein | 386 | 40% helix, 1% strand | A0A0J4U551 |
| F | Non-template promoter DNA | dna | 25 | — | — |
| G | Template DNA promoter | dna | 29 | — | — |
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 | 1150 | 0.84 | 0.85 | 116 | empty |
| 2 | 628 | 0.81 | 0.86 | 79 | empty |
| 3 | 980 | 0.81 | 0.82 | 105 | empty |
| 4 | 950 | 0.78 | 0.81 | 91 | empty |
| 5 | 739 | 0.78 | 0.82 | 99 | empty |
Interfaces
12 interfaces between chains.
- C–D · 7032 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 1880 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 1504 Ų buried · 11 hydrogen bonds · protein-protein
- F–G · 1218 Ų buried · 120 hydrogen bonds · nucleic-nucleic
- D–E · 1208 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5NSR · Cryo-EM structure of RNA polymerase-sigma54 holo enzyme with promoter DNA closed complex · 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
- P0A8T7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T7) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 5NSR · PDBe 5NSR · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt A0A0J4U551
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