Research workbench
Cryoem structure of E.COLI RNA polymerase elongation complex bound with rfah
Analyse Cryoem structure of E.COLI RNA polymerase elongation complex bound with rfah in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C6S
- Type
- protein + DNA + RNA
- Length
- 3,428 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (29-mer); RNA (5'- R(*GP*CP*AP*UP*UP*CP*AP*AP*AP*GP*CP*CP*GP*AP*GP*AP*GP*GP*UP*A)-3')…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, P0A800, P0AFW0
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 9 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (29-mer) | dna | 29 | — | — |
| B | DNA (29-mer) | dna | 29 | — | — |
| R | RNA (5'- R(*GP*CP*AP*UP*UP*CP*AP*AP*AP*GP*CP*CP*GP*AP*GP*AP*GP*GP*UP*A)-3') | rna | 10 | — | — |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 221 | 22% helix, 36% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 219 | 19% helix, 37% 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 | 1335 | 36% helix, 17% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 83 | 63% helix, 0% strand | P0A800 |
| D | Transcription antitermination protein rfah | protein | 161 | 15% helix, 34% strand | P0AFW0 |
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 | 688 | 0.82 | 0.87 | 71 | empty |
| 2 | 837 | 0.82 | 0.85 | 75 | empty |
| 3 | 387 | 0.80 | 0.90 | 50 | empty |
| 4 | 1040 | 0.80 | 0.82 | 97 | empty |
| 5 | 572 | 0.80 | 0.86 | 65 | empty |
Interfaces
19 interfaces between chains.
- I–J · 8478 Ų buried · 97 hydrogen bonds · protein-protein
- G–I · 1915 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1857 Ų buried · 11 hydrogen bonds · protein-protein
- J–K · 1284 Ų buried · 16 hydrogen bonds · protein-protein
- J–D · 1062 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6C6S · CryoEM structure of E.coli RNA polymerase elongation complex bound with RfaH · the same entry in another collection · chain D against D, 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 0.98
- P0AFW0 · AlphaFold monomer V2.0 prediction for transcription antitermination protein rfah (P0AFW0) · a predicted model of the same protein · chain D against A, TM-score 0.56
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 P0AFW0
- Elsewhere: RCSB PDB 6C6S · PDBe 6C6S · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P0AFW0
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