Research workbench
Cryo-EM structure of ecmrr-rnap-promoter initial transcribing complex with 3-nt RNA transcript (ecmrr-rpitc-3NT)
Analyse Cryo-EM structure of ecmrr-rnap-promoter initial transcribing complex with 3-nt… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XL9
- Type
- protein + DNA + RNA
- Length
- 4,248 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
- P0A7Z6, B7MIX3, P0A8T8, P00579
- Ligands
- 118, ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 9 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 20% helix, 38% strand | P0A7Z6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 229 | 19% helix, 44% strand | P0A7Z6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1339 | 28% helix, 24% strand | B7MIX3 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1338 | 35% helix, 17% strand | P0A8T8 |
| F | RNA polymerase sigma factor rpod | protein | 465 | 65% helix, 1% strand | P00579 |
| N | Synthetic non-template strand DNA (54-mer) | dna | 54 | — | — |
| R | RNA (5'-D(*(GTP))-R(P*AP*G)-3') | rna | 3 | — | — |
| T | Synthetic template strand DNA (54-mer) | dna | 54 | — | — |
| G, H | Merr family transcriptional regulator ecmrr | protein | 268 | 41% helix, 26% strand | — |
Ligands and binding sites
- 118 · Tetraphenylantimonium ion · ligand · 3 copies · chains F, N, T, G, H
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · 2 copies · 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 | 971 | 0.86 | 0.88 | 126 | empty |
| 2 | 648 | 0.83 | 0.88 | 55 | empty |
| 3 | 1054 | 0.80 | 0.82 | 80 | empty |
| 4 | 772 | 0.77 | 0.81 | 66 | empty |
| 5 | 530 | 0.77 | 0.84 | 60 | empty |
Interfaces
24 interfaces between chains.
- C–D · 8076 Ų buried · 73 hydrogen bonds · protein-protein
- D–F · 2564 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 2315 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 2056 Ų buried · 9 hydrogen bonds · protein-protein
- C–F · 1946 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6XL9 · Cryo-EM structure of EcmrR-RNAP-promoter initial transcribing complex with 3-nt RNA… · the same entry in another collection · chain H against H, 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 0.96
- P0A7Z6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (P0A7Z6) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P00579
- Elsewhere: RCSB PDB 6XL9 · PDBe 6XL9 · UniProt P0A7Z6 · UniProt B7MIX3 · UniProt P0A8T8 · UniProt P00579
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