Research workbench
The cryo-EM structure of E. COLI cuer transcription activation complex with fully duplex promoter DNA
Analyse The cryo-EM structure of E. COLI cuer transcription activation complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C17
- Type
- protein + DNA
- Length
- 4,099 residues
- Chains
- 10
- 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, P00579, P0A9G4
- Ligands
- ZN, MG, AG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 10 distinct chains · 36% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 303 | 25% helix, 25% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 18% helix, 26% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1338 | 29% helix, 19% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1331 | 33% helix, 13% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 61% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 465 | 67% helix, 0% strand | P00579 |
| 1 | DNA (72-mer) | dna | 58 | — | — |
| 2 | DNA (72-mer) | dna | 46 | — | — |
| G | Hth-type transcriptional regulator cuer | protein | 127 | 57% helix, 2% strand | P0A9G4 |
| H | Hth-type transcriptional regulator cuer | protein | 128 | 59% helix, 4% strand | P0A9G4 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · chains D
- AG · Silver ion · metal · chains G, H
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 | 735 | 0.86 | 0.90 | 89 | empty |
| 2 | 674 | 0.84 | 0.89 | 77 | empty |
| 3 | 1038 | 0.83 | 0.84 | 89 | empty |
| 4 | 1165 | 0.83 | 0.84 | 76 | empty |
| 5 | 372 | 0.82 | 0.92 | 43 | empty |
Interfaces
26 interfaces between chains.
- C–D · 9029 Ų buried · 103 hydrogen bonds · protein-protein
- D–F · 3110 Ų buried · 38 hydrogen bonds · protein-protein
- C–F · 2751 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 2241 Ų buried · 28 hydrogen bonds · protein-protein
- 1–2 · 2086 Ų buried · 162 hydrogen bonds · nucleic-nucleic
Compared structures
- 7C17 · The cryo-EM structure of E. coli CueR transcription activation complex with fully duplex… · the same entry in another collection · chain H against H, TM-score 1.00
- P0A9G4 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator cuer (P0A9G4) · a predicted model of the same protein · chain H against A, TM-score 0.84
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
- Every structure of UniProt P0A9G4
- Elsewhere: RCSB PDB 7C17 · PDBe 7C17 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579 · UniProt P0A9G4
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