7R4Q
The SARS-CoV-2 spike in complex with the 1.29 neutralizing nanobody
- PDB DOI: https://doi.org/10.2210/pdb7R4Q/pdb
- EM Map EMD-14314: EMDB EMDataResource
- Classification: VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Camelus dromedarius
- Expression System: Mammalian expression vector Flag-MCS-pcDNA3.1
- Mutation(s): Yes 
- Deposited: 2022-02-09 Released: 2022-06-08 
- Funding Organization(s): Ministry of Economy and Competitiveness (MINECO), European Union (EU)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.60 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
wwPDB Validation   3D Report Full Report
This is version 1.0 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Spike glycoprotein | 1,264 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 6  Gene Names: S, 2 | ||
UniProt | |||||
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2  Go to UniProtKB:  P0DTC2 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P0DTC2 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Camel-derived nanobody 1.29 | 126 | Camelus dromedarius | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.60 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
MODEL REFINEMENT | PHENIX | 1.17.1_3660 |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-06-08  Deposition Author(s): Casasnovas, J.M., Melero, R., Arranz, R., Fernandez, L.A.
Funding Organization | Location | Grant Number |
---|---|---|
Ministry of Economy and Competitiveness (MINECO) | Spain | 202020E079 |
European Union (EU) | European Union | ESFRI-2019-01-CSIC-16 |
Revision History (Full details and data files)
- Version 1.0: 2022-06-08
Type: Initial release