Download MendeleyCrystal structure of SARS-CoV-1 RBD in complex with nanobody aSR29 and aSR347
Zeng, W.H., Ma, H., Jin, T.C.To be published.
8WCG
Crystal structure of SARS-CoV-1 RBD in complex with nanobody aSR29 and aSR347
- PDB DOI: https://doi.org/10.2210/pdb8WCG/pdb
- Classification: ANTIVIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus, Vicugna pacos
- Expression System: Homo sapiens
- Mutation(s): No
- Deposited: 2023-09-12 Released: 2024-09-18
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.279 (Depositor), 0.279 (DCC)
- R-Value Work: 0.232 (Depositor), 0.232 (DCC)
- R-Value Observed: 0.235 (Depositor)
Starting Models: experimental
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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
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Spike protein S1 | A, C [auth B] | 197 | Severe acute respiratory syndrome coronavirus | Mutation(s): 0 Gene Names: S, 2 |  |
UniProt | |||||
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus) Explore P59594 Go to UniProtKB: P59594 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P59594 | ||||
Glycosylation | |||||
| Glycosylation Sites: 1 | Go to GlyGen: P59594-1 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| aSR29 nanobody | B [auth C], D | 127 | Vicugna pacos | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| aSR347 nanobody | E [auth b], F [auth E] | 131 | Vicugna pacos | Mutation(s): 0 |  |
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| NAG (Subject of Investigation/LOI) Query on NAG | G [auth A], H [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.60 Å
- R-Value Free: 0.279 (Depositor), 0.279 (DCC)
- R-Value Work: 0.232 (Depositor), 0.232 (DCC)
- R-Value Observed: 0.235 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 76.852 | α = 90 |
| b = 134.679 | β = 90 |
| c = 136.688 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XSCALE | data scaling |
| autoPROC | data reduction |
| PHENIX | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2024-09-18 Deposition Author(s): Zeng, W.H., Ma, H., Jin, T.C.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Natural Science Foundation of China (NSFC) | China | 32100745 |
| National Natural Science Foundation of China (NSFC) | China | 82272301 |
Revision History (Full details and data files)
- Version 1.0: 2024-09-18
Type: Initial release - Version 1.1: 2024-11-13
Changes: Structure summary
