7L02
Cryo-EM structure of SARS-CoV-2 2P S ectodomain bound to one copy of domain-swapped antibody 2G12
- PDB DOI: https://doi.org/10.2210/pdb7L02/pdb
- EM Map EMD-23094: EMDB EMDataResource
- Classification: VIRAL PROTEIN/IMMUNE SYSTEM
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2020-12-10 Released: 2020-12-30 
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 3.20 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 | 1,121 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0  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 |
2G12 heavy chain | D [auth H], G [auth M] | 226 | 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 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
2G12 light chain | E [auth K], F [auth L] | 213 | Homo sapiens | 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 | H [auth D], K [auth G], L [auth I], M [auth J], N, H [auth D], K [auth G], L [auth I], M [auth J], N, O, P, Q, R, S | 2 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT |
Entity ID: 5 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | I [auth E] | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Entity ID: 6 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[beta-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 | J [auth F] | 8 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G14481TB GlyCosmos:  G14481TB GlyGen:  G14481TB |
Entity ID: 7 | |||||
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Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | T | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G51945PF GlyCosmos:  G51945PF GlyGen:  G51945PF |
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 B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: ELECTRON MICROSCOPY
- Resolution: 3.20 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | cryoSPARC | |
MODEL REFINEMENT | PHENIX | |
MODEL REFINEMENT | ISOLDE | |
MODEL REFINEMENT | Coot |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-12-30  Deposition Author(s): Manne, K., Henderson, R., Acharya, P.
Funding Organization | Location | Grant Number |
---|---|---|
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | AI145687 |
Revision History (Full details and data files)
- Version 1.0: 2020-12-30
Type: Initial release - Version 1.1: 2021-06-02
Changes: Database references - Version 1.2: 2021-06-09
Changes: Database references