Research workbench
Cryoem structure of E.COLI RNA polymerase paused elongation complex bound to nusa
Analyse Cryoem structure of E.COLI RNA polymerase paused elongation complex bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FLQ
- Type
- protein + DNA + RNA
- Length
- 3,959 residues
- Chains
- 9
- 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, P0AFF6
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 9 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 310 | 27% helix, 19% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 298 | 24% helix, 20% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 28% helix, 21% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1334 | 34% helix, 17% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 90 | 68% helix, 0% strand | P0A800 |
| F | Transcription TERMINATION/ANTITERMINATION protein nusa | protein | 495 | 43% helix, 17% strand | P0AFF6 |
| N | DNA (31-mer) | dna | 31 | — | — |
| R | RNA (5'- R(*CP*CP*UP*GP*AP*UP*CP*AP*GP*GP*CP*GP*AP*UP*GP*UP*GP*UP*GP*CP*U)- 3') | rna | 21 | — | — |
| T | DNA (39-mer) | dna | 39 | — | — |
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 | 831 | 0.83 | 0.86 | 78 | empty |
| 2 | 821 | 0.82 | 0.84 | 75 | empty |
| 3 | 514 | 0.80 | 0.87 | 55 | empty |
| 4 | 429 | 0.80 | 0.89 | 44 | empty |
| 5 | 887 | 0.78 | 0.81 | 88 | empty |
Interfaces
19 interfaces between chains.
- C–D · 8478 Ų buried · 83 hydrogen bonds · protein-protein
- A–B · 1822 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 1769 Ų buried · 12 hydrogen bonds · protein-protein
- N–T · 1321 Ų buried · 111 hydrogen bonds · nucleic-nucleic
- D–E · 1228 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6FLQ · CryoEM structure of E.coli RNA polymerase paused elongation complex bound to NusA · the same entry in another collection · chain T against T, 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 C against A, TM-score 0.95
- P0AFF6 · AlphaFold monomer V2.0 prediction for transcription TERMINATION/ANTITERMINATION protein… · a predicted model of the same protein · chain F against A, TM-score 0.76
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 P0AFF6
- Elsewhere: RCSB PDB 6FLQ · PDBe 6FLQ · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P0AFF6
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