7QO7
SARS-CoV-2 S Omicron Spike B.1.1.529
- PDB DOI: https://doi.org/10.2210/pdb7QO7/pdb
- EM Map EMD-14086: EMDB EMDataResource
- Classification: VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2
- Expression System: Cricetulus griseus
- Mutation(s): No 
- Deposited: 2021-12-23 Released: 2022-01-19 
- Funding Organization(s): Swiss National Science Foundation
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.02 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 |
Surface glycoprotein,Fibritin,SARS-CoV-2 S Omicron Spike B.1.1.529 | 1,285 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0  | ||
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 |
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E, H, M | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | F, G, I, J, K F, G, I, J, K, L, N, O, P, Q, R, S, T, U, V, W, X, Z | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
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: 3.02 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
MODEL REFINEMENT | PHENIX | |
RECONSTRUCTION | cryoSPARC | 3.3.1 |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-01-19  Deposition Author(s): Ni, D., Lau, K., Turelli, P., Beckert, B., Nazarov, S., Pojer, F., Myasnikov, A., Stahlberg, H., Trono, D.
Funding Organization | Location | Grant Number |
---|---|---|
Swiss National Science Foundation | Switzerland | -- |
Revision History (Full details and data files)
- Version 1.0: 2022-01-19
Type: Initial release