7UZ8
Structure of the SARS-CoV-2 Omicron BA.1 S 6P trimer in complex with the mouse antibody Fab fragment, M8a-31
- PDB DOI: https://doi.org/10.2210/pdb7UZ8/pdb
- EM Map EMD-26882: EMDB EMDataResource
- Classification: IMMUNE SYSTEM/VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Mus musculus
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Deposited: 2022-05-08 Released: 2022-12-07 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.10 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 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Spike glycoprotein | 1,253 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 40  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 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
M8a-31 Fab heavy chain | D [auth H], F [auth M], H [auth P] | 228 | Mus musculus | 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 |
M8a-31 Fab light chain | E [auth L], G [auth N], I [auth Q] | 220 | Mus musculus | Mutation(s): 0  | |
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | J [auth D], K [auth E], L [auth F] | 2 | N/A | 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 (Subject of Investigation/LOI) Query on NAG | AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.10 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | cryoSPARC | 3.2 |
MODEL REFINEMENT | PHENIX | 1.19.2 |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-12-07  Deposition Author(s): Fan, C., Bjorkman, P.J.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | 1P01AI138938-S1 |
Revision History (Full details and data files)
- Version 1.0: 2022-12-07
Type: Initial release - Version 1.1: 2022-12-14
Changes: Database references - Version 1.2: 2022-12-28
Changes: Database references