Research workbench
CryoEM structure of E.coli RNA polymerase elongation complex bound to NusA and NusG (NusA and NusG elongation complex in less-swiveled conformation)
Analyse CryoEM structure of E.coli RNA polymerase elongation complex bound to NusA and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PY6
- Type
- protein + DNA + RNA
- Length
- 3,899 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.1
- Source
- Escherichia coli; SYNTHETIC CONSTRUCT
- Molecule
- ntDNA; tDNA; RNA; DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V4, P0A8T8, P0A800, P0AFG0, P0AFF6
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 4.1 · 10 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | ntDNA | dna | 26 | — | — |
| T | tDNA | dna | 30 | — | — |
| R | RNA | rna | 11 | — | — |
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 21% helix, 30% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 220 | 20% helix, 34% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 31% helix, 21% strand | P0A8V4 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1335 | 37% helix, 16% strand | P0A8T8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 90 | 66% helix, 0% strand | P0A800 |
| G | Transcription termination/antitermination protein NusG | protein | 123 | 30% helix, 16% strand | P0AFG0 |
| F | Transcription termination/antitermination protein NusA | protein | 495 | 28% helix, 8% strand | P0AFF6 |
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 | 949 | 0.85 | 0.87 | 102 | empty |
| 2 | 972 | 0.84 | 0.86 | 82 | empty |
| 3 | 624 | 0.82 | 0.87 | 68 | empty |
| 4 | 652 | 0.79 | 0.84 | 70 | empty |
| 5 | 701 | 0.78 | 0.83 | 78 | empty |
Interfaces
20 interfaces between chains.
- C–D · 8324 Ų buried · 79 hydrogen bonds · protein-protein
- A–B · 2029 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1950 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 1389 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1106 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7PY6 · Cryoem structure of E.COLI RNA polymerase elongation complex bound to nusa and nusg (nusa… · the same entry in another collection · chain T against T, TM-score 1.00
- P0A8V4 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V4) · a predicted model of the same protein · chain C against A, TM-score 0.98
- 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
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 P0A8V4
- Every structure of UniProt P0A8T8
- Every structure of UniProt P0A800
- Every structure of UniProt P0AFG0
- Every structure of UniProt P0AFF6
- Elsewhere: RCSB PDB 7PY6 · PDBe 7PY6 · UniProt P0A7Z4 · UniProt P0A8V4 · UniProt P0A8T8 · UniProt P0A800 · UniProt P0AFG0 · UniProt P0AFF6
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