A broadly neutralizing antibody against SARS-CoV-2 Omicron variants
Planchais, C., Fernandez, I., Rey, F.A., Mouquet, H.To be published.
8QH0
Crystal structure of the SARS-CoV-2 RBD with the antibody Cv2.3194
- PDB DOI: https://doi.org/10.2210/pdb8QH0/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
- Expression System: Drosophila melanogaster, Homo sapiens
- Mutation(s): Yes
- Deposited: 2023-09-06 Released: 2024-06-19
- Funding Organization(s): Not funded
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.87 Å
- R-Value Free: 0.209
- R-Value Work: 0.185
- R-Value Observed: 0.186
Starting Models: experimental, in silico
View more details
wwPDB Validation 3D Report Full Report
This is version 1.1 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Molecule | Chains | Sequence Length | Organism | Details | Image |
|---|---|---|---|---|---|
| Spike protein S1 | 206 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 1 Gene Names: S, 2 | ||
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2 | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0DTC2 | ||||
| Glycosylation Sites: 1 | Go to GlyGen: P0DTC2-1 | ||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Molecule | Chains | Sequence Length | Organism | Details | Image |
|---|---|---|---|---|---|
| Cv2.3194 Heavy chain | B [auth H] | 229 | Homo sapiens | Mutation(s): 0 | |
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| |||||
Find similar proteins by:
(by identity cutoff) | 3D Structure
| Molecule | Chains | Sequence Length | Organism | Details | Image |
|---|---|---|---|---|---|
| IGK@ protein | C [auth L] | 211 | Homo sapiens | Mutation(s): 0 Gene Names: IGK@ | |
Find proteins for Q6PJF2 (Homo sapiens) Explore Q6PJF2 Go to UniProtKB: Q6PJF2 | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q6PJF2 | ||||
| |||||
Oligosaccharides
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PRO Query on PRO | E [auth A] | PROLINE C5 H9 N O2 ONIBWKKTOPOVIA-BYPYZUCNSA-N | |||
| GOL Query on GOL | F [auth A], G [auth H] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.87 Å
- R-Value Free: 0.209
- R-Value Work: 0.185
- R-Value Observed: 0.186
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 54.388 | α = 90 |
| b = 89.186 | β = 90 |
| c = 174.471 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-06-19 Deposition Author(s): Fernandez, I., Rey, F.A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Not funded | -- |
Revision History (Full details and data files)
- Version 1.0: 2024-06-19
Type: Initial release - Version 1.1: 2024-11-20
Changes: Structure summary