7XOD
SARS-CoV-2 Omicron BA.2 Variant Spike Trimer with three JMB2002 Fab Bound
- PDB DOI: https://doi.org/10.2210/pdb7XOD/pdb
- EM Map EMD-33345: EMDB EMDataResource
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens, Lama glama
- Expression System: Homo sapiens, Mesocricetus auratus, Escherichia coli
- Mutation(s): Yes 
- Deposited: 2022-05-01 Released: 2022-06-15 
- Funding Organization(s): National Natural Science Foundation of China (NSFC)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.27 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 | 1,270 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 37  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 |
Heavy chain of JMB2002 Fab | D [auth X], G [auth U], J [auth R] | 229 | Homo sapiens | 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 |
Light chain of JMB2002 Fab | E [auth Y], H [auth V], K [auth S] | 214 | Homo sapiens | 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: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Nanobody | F [auth Z], I [auth W], L [auth T] | 124 | Lama glama | 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: 3.27 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Entry History & Funding Information
Deposition Data
- Released Date: 2022-06-15  Deposition Author(s): Xu, Y., Wu, C., Liu, H., Yin, W., Xu, H.E.
Funding Organization | Location | Grant Number |
---|---|---|
National Natural Science Foundation of China (NSFC) | China | 81902085 |
National Natural Science Foundation of China (NSFC) | China | 32130022 |
National Natural Science Foundation of China (NSFC) | China | 32171189 |
National Natural Science Foundation of China (NSFC) | China | 82122067 |
Revision History (Full details and data files)
- Version 1.0: 2022-06-15
Type: Initial release - Version 1.1: 2022-06-22
Changes: Database references - Version 1.2: 2022-07-13
Changes: Database references