MolNFT v1 · #169738 · protein + DNA + RNA
Cryo-EM structure of E. COLI rnap-DNA elongation complex 2 (RDE2) in ecmrr-dependent transcription
6XLN · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of E. COLI rnap-DNA elongation complex 2 (RDE2) in ecmrr-dependent transcription”. Electron microscopy, 3 ligands (1N7, ZN, MG), 20 pockets (best druggability 0.82).…
- PDB
- 6XLN
- Type
- protein + DNA + RNA
- Length
- 3,247 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
- P0A7Z6, B7MIX3, P0A8T8, B7MFL0
- Ligands
- 1N7, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 8 distinct chains · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 22% helix, 39% strand | P0A7Z6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 22% helix, 45% strand | P0A7Z6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1339 | 31% helix, 25% strand | B7MIX3 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1336 | 37% helix, 21% strand | P0A8T8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 62% helix, 0% strand | B7MFL0 |
| N | Synthetic non-template strand DNA (54-mer) | dna | 14 | — | — |
| T | Synthetic template strand DNA (54-mer) | dna | 17 | — | — |
| R | 9-nt RNA transcript | rna | 9 | — | — |
Ligands and binding sites
- 1N7 · Chapso · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · chains D, R
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 | 774 | 0.82 | 0.85 | 79 | 1N7 |
| 2 | 391 | 0.81 | 0.90 | 48 | empty |
| 3 | 522 | 0.81 | 0.87 | 60 | empty |
| 4 | 802 | 0.78 | 0.82 | 79 | empty |
| 5 | 1100 | 0.77 | 0.79 | 87 | empty |
Interfaces
15 interfaces between chains.
- C–D · 8139 Ų buried · 109 hydrogen bonds · protein-protein
- A–B · 2132 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1842 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 1252 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1005 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6XLN · Cryo-EM structure of E. coli RNAP-DNA elongation complex 2 (RDe2) in EcmrR-dependent… · the same entry in another collection · chain R against R, TM-score 1.00
- B7MIX3 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (B7MIX3) · a predicted model of the same protein · chain C against A, TM-score 0.99
- B7MFL0 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (B7MFL0) · a predicted model of the same protein · chain E against A, TM-score 0.95
- P0A8T8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T8) · a predicted model of the same protein · chain D against A, TM-score 0.93
- P0A7Z6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (P0A7Z6) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 P0A7Z6
- Every structure of UniProt B7MIX3
- Every structure of UniProt P0A8T8
- Every structure of UniProt B7MFL0
- Elsewhere: RCSB PDB 6XLN · PDBe 6XLN · UniProt P0A7Z6 · UniProt B7MIX3 · UniProt P0A8T8 · UniProt B7MFL0
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