6ZXN
Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1)
- PDB DOI: https://doi.org/10.2210/pdb6ZXN/pdb
- EM Map EMD-11526: EMDB EMDataResource
- Classification: VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2, Vicugna pacos
- Expression System: Homo sapiens, Escherichia coli
- Mutation(s): No 
- Deposited: 2020-07-30 Released: 2020-09-23 
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 2.93 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 |
Spike glycoprotein | 1,288 | 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 |
Nanobody Ty1 | 134 | Vicugna pacos | Mutation(s): 0  | ||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 | G, H, I, J, K G, H, I, J, K, L, M, N, O, P, Q, R | 2 | 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 Query on NAG | AA [auth A] AB [auth C] BA [auth A] BB [auth C] CA [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: 2.93 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | cryoSPARC | 2.15 |
MODEL REFINEMENT | PHENIX |
Entry History 
Deposition Data
- Released Date: 2020-09-23  Deposition Author(s): Hallberg, B.M., Das, H.
Revision History (Full details and data files)
- Version 1.0: 2020-09-23
Type: Initial release