7JWY
Structure of SARS-CoV-2 spike at pH 4.5
- PDB DOI: https://doi.org/10.2210/pdb7JWY/pdb
- EM Map EMD-22515: EMDB EMDataResource
- Classification: VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Membrane Protein: Yes  mpstruc
- Deposited: 2020-08-26 Released: 2020-11-25 
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 2.50 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
wwPDB Validation   3D Report Full Report
This is version 1.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Spike glycoprotein | 1,275 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 5  Gene Names: S, 2 Membrane Entity: Yes  | ||
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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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D, E, F, G, H D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 2.50 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | RELION | 3.0.8 |
MODEL REFINEMENT | PHENIX |
Entry History 
Deposition Data
- Released Date: 2020-11-25  Deposition Author(s): Zhou, T., Tsybovsky, Y., Kwong, P.D.
Revision History (Full details and data files)
- Version 1.0: 2020-11-25
Type: Initial release - Version 1.1: 2021-10-06
Changes: Database references - Version 1.2: 2021-12-15
Changes: Database references