6ZGE
Uncleavable Spike Protein of SARS-CoV-2 in Closed Conformation
- PDB DOI: https://doi.org/10.2210/pdb6ZGE/pdb
- EM Map EMD-11203: EMDB EMDataResource
- Classification: VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2
- Expression System: Homo sapiens
- Mutation(s): Yes 
- Deposited: 2020-06-18 Released: 2020-07-01 
- Funding Organization(s): The Francis Crick Institute
Experimental Data Snapshot
- Method: ELECTRON MICROSCOPY
- Resolution: 2.60 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Spike glycoprotein | 1,287 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 4  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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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | AA [auth a], BA [auth b], CA [auth c], D, DA [auth d], AA [auth a], BA [auth b], CA [auth c], D, DA [auth d], E, EA [auth e], F, FA [auth f], G, GA [auth g], H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z | 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 | AB [auth C] BB [auth C] HA [auth A] IA [auth A] JA [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: 2.60 Å
- Aggregation State: PARTICLE 
- Reconstruction Method: SINGLE PARTICLE 
Task | Software Package | Version |
---|---|---|
RECONSTRUCTION | cryoSPARC | 2.15 |
MODEL REFINEMENT | PHENIX | 1.18 |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-07-01  Deposition Author(s): Wrobel, A.G., Benton, D.J., Rosenthal, P.B., Gamblin, S.J.
Funding Organization | Location | Grant Number |
---|---|---|
The Francis Crick Institute | United Kingdom | FC001078 |
The Francis Crick Institute | United Kingdom | FC001143 |
Revision History (Full details and data files)
- Version 1.0: 2020-07-01
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2020-09-16
Changes: Database references, Structure summary