Research workbench
Cryo-EM structure of an extended SARS-CoV-2 replication and transcription complex reveals an intermediate state in cap synthesis
Analyse Cryo-EM structure of an extended SARS-CoV-2 replication and transcription… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CYQ
- Type
- protein + RNA
- Length
- 2,707 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.83
- Source
- Severe acute respiratory syndrome coronavirus 2; SYNTHETIC CONSTRUCT
- Molecule
- RNA-directed RNA polymerase; Non-structural protein 8; Non-structural protein 7; Primer…
- EC
- 2.7.7.48, 3.6.4.12, 3.6.4.13
- UniProt
- P0DTD1
- Ligands
- GDP, ZN, MG
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · resolution 2.83 · 9 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA-directed RNA polymerase (EC 2.7.7.48) | protein | 926 | 41% helix, 18% strand | P0DTD1 |
| B | Non-structural protein 8 | protein | 187 | 50% helix, 16% strand | P0DTD1 |
| C | Non-structural protein 7 | protein | 72 | 75% helix, 0% strand | P0DTD1 |
| D | Non-structural protein 8 | protein | 186 | 44% helix, 15% strand | P0DTD1 |
| I | Primer | rna | 25 | — | — |
| J | Template | rna | 27 | — | — |
| F | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 585 | 21% helix, 18% strand | P0DTD1 |
| E | Helicase (EC 3.6.4.12, 3.6.4.13) | protein | 586 | 21% helix, 17% strand | P0DTD1 |
| G | Non-structural protein 9 | protein | 113 | 15% helix, 44% strand | P0DTD1 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A, G
- ZN · Zinc ion · metal · 8 copies · chains A, F, E
- MG · Magnesium ion · metal · chains A, G
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 | 134 | 0.79 | 0.97 | 24 | empty |
| 2 | 983 | 0.79 | 0.81 | 79 | empty |
| 3 | 464 | 0.74 | 0.83 | 46 | empty |
| 4 | 441 | 0.74 | 0.83 | 44 | empty |
| 5 | 577 | 0.72 | 0.80 | 41 | empty |
Interfaces
19 interfaces between chains.
- A–B · 2561 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1416 Ų buried · 5 hydrogen bonds · protein-protein
- I–J · 1169 Ų buried · 134 hydrogen bonds · nucleic-nucleic
- A–J · 1104 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–G · 949 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7CYQ · Cryo-EM structure of an extended SARS-cov-2 replication and transcription complex reveals… · the same entry in another collection · chain A against A, TM-score 1.00
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 P0DTD1
- Elsewhere: RCSB PDB 7CYQ · PDBe 7CYQ · UniProt P0DTD1
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