Research workbench
Cryo-EM structure of sigma70 bound HK022 putRNA-associated E.coli RNA polymerase elongation complex
Analyse Cryo-EM structure of sigma70 bound HK022 putRNA-associated E.coli RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XUI
- Type
- protein + DNA + RNA
- Length
- 3,584 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.61
- Source
- Escherichia coli K-12; SYNTHETIC CONSTRUCT
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 3.61 · 8 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 18% helix, 31% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 19% helix, 28% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 29% helix, 21% strand | P0A8V2 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1336 | 37% helix, 15% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 59% helix, 0% strand | P0A800 |
| L | RNA polymerase sigma factor RpoD | protein | 269 | 75% helix, 0% strand | P00579 |
| B | template DNA | dna | 10 | — | — |
| R | RNA (122-mer) | rna | 101 | — | — |
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 | 747 | 0.82 | 0.86 | 69 | empty |
| 2 | 713 | 0.82 | 0.86 | 76 | empty |
| 3 | 741 | 0.79 | 0.83 | 74 | empty |
| 4 | 700 | 0.77 | 0.83 | 87 | empty |
| 5 | 263 | 0.77 | 0.89 | 33 | empty |
Interfaces
13 interfaces between chains.
- I–J · 8101 Ų buried · 66 hydrogen bonds · protein-protein
- G–H · 1989 Ų buried · 9 hydrogen bonds · protein-protein
- G–I · 1655 Ų buried · 14 hydrogen bonds · protein-protein
- J–R · 1460 Ų buried · 32 hydrogen bonds · protein-nucleic
- J–K · 1433 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7XUI · Cryo-EM structure of SIGMA70 bound HK022 putrna-associated E.COLI RNA polymerase… · 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 I 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 J against A, TM-score 0.85
- P00579 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor rpod (P00579) · a predicted model of the same protein · chain L against A, TM-score 0.85
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 P00579
- Elsewhere: RCSB PDB 7XUI · PDBe 7XUI · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579
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