Research workbench
The cryo-EM structure of C. crescentus GcrA-TACdown
Analyse The cryo-EM structure of C. crescentus GcrA-TACdown in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7YE2
- Type
- protein + DNA
- Length
- 3,724 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.8
- Source
- Caulobacter vibrioides NA1000; SYNTHETIC CONSTRUCT
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- B8H4F8, B8GZW7, A0A0H3C4W8, B8H618, A0A0H3CAV3, A0A0H3C9J4
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 3.8 · 9 distinct chains · 36% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 306 | 21% helix, 15% strand | B8H4F8 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 220 | 18% helix, 16% strand | B8H4F8 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1303 | 28% helix, 15% strand | B8GZW7 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1140 | 41% helix, 11% strand | A0A0H3C4W8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 69 | 58% helix, 0% strand | B8H618 |
| F | RNA polymerase sigma factor RpoD | protein | 497 | 64% helix, 1% strand | A0A0H3CAV3 |
| H | DNA (90-MER)-non template | dna | 68 | — | — |
| I | DNA (90-MER)-template | dna | 68 | — | — |
| G | Cell cycle regulatory protein GcrA | protein | 53 | 13% helix, 13% strand | A0A0H3C9J4 |
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 | 838 | 0.85 | 0.87 | 98 | empty |
| 2 | 456 | 0.84 | 0.92 | 49 | empty |
| 3 | 658 | 0.83 | 0.88 | 87 | empty |
| 4 | 293 | 0.80 | 0.91 | 37 | empty |
| 5 | 1147 | 0.79 | 0.81 | 84 | empty |
Interfaces
24 interfaces between chains.
- C–D · 8505 Ų buried · 88 hydrogen bonds · protein-protein
- D–F · 3229 Ų buried · 21 hydrogen bonds · protein-protein
- H–I · 2506 Ų buried · 178 hydrogen bonds · nucleic-nucleic
- A–B · 2456 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 2456 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- B8GZW7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (B8GZW7) · a predicted model of the same protein · chain C against A, TM-score 0.97
- B8H4F8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (B8H4F8) · a predicted model of the same protein · chain B against A, TM-score 0.90
- B8H618 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (B8H618) · a predicted model of the same protein · chain E against A, TM-score 0.87
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 B8H4F8
- Every structure of UniProt B8GZW7
- Every structure of UniProt A0A0H3C4W8
- Every structure of UniProt B8H618
- Every structure of UniProt A0A0H3CAV3
- Every structure of UniProt A0A0H3C9J4
- Elsewhere: RCSB PDB 7YE2 · PDBe 7YE2 · UniProt B8H4F8 · UniProt B8GZW7 · UniProt A0A0H3C4W8 · UniProt B8H618 · UniProt A0A0H3CAV3 · UniProt A0A0H3C9J4
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