7SN3
Structure of human SARS-CoV-2 spike glycoprotein trimer bound by neutralizing antibody C1C-A3 Fab (variable region)
- PDB DOI: https://doi.org/10.2210/pdb7SN3/pdb
- EM Map EMD-25210: EMDB EMDataResource
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Deposited: 2021-10-27 Released: 2021-12-08 
- Funding Organization(s): Other private
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 | 1,273 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 9  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 |
neutralizing antibody C1C-A3 heavy chain variable region | 250 | Homo sapiens | Mutation(s): 0  Gene Names: IGHV3-33 | ||
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 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
neutralizing antibody C1C-A3 light chain variable region | E, G, I [auth L] | 238 | Homo sapiens | Mutation(s): 0  Gene Names: IGKV3-11 | |
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 |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | J [auth I], K [auth J], L [auth K] | 3 | N/A | 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] AB [auth C] BA [auth B] BB [auth C] CA [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: 3.10 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
MODEL REFINEMENT | PHENIX | 1.19-4080 |
RECONSTRUCTION | cryoSPARC | 2.14.2 |
Entry History & Funding Information
Deposition Data
- Released Date: 2021-12-08  Deposition Author(s): Pan, J., Abraham, J., Shankar, S.
Funding Organization | Location | Grant Number |
---|---|---|
Other private | United States | no grant number |
Revision History (Full details and data files)
- Version 1.0: 2021-12-08
Type: Initial release - Version 1.1: 2021-12-15
Changes: Database references - Version 1.2: 2022-02-02
Changes: Database references