8CSA | pdb_00008csa

Triple mutant (K417N-E484K-N501Y) SARS-CoV-2 spike protein in the 3-RBD-Down conformation (S-GSAS-D614G-K417N-E484K-N501Y)

PDB DOI: https://doi.org/10.2210/pdb8CSA/pdb
EM Map EMD-26961: EMDB EMDataResource

Classification: VIRAL PROTEIN
Organism(s): Severe acute respiratory syndrome coronavirus 2
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2022-05-12 Released: 2022-07-20
Deposition Author(s): Gobeil, S., Acharya, P.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8CSA

This is version 1.3 of the entry. See complete history.

Literature

Effect of natural mutations of SARS-CoV-2 on spike structure, conformation, and antigenicity

Gobeil, S.M.-C., Janowska, K., McDowell, S., Mansouri, K., Parks, R., Stalls, V., Kopp, M.F., Manne, K., Li, D., Wiehe, K., Saunders, K., Edwards, R.J., Korber, B., Haynes, B.F., Henderson, R.C., Acharya, P.

(2021) Science

DOI: https://doi.org/10.1126/science.abi6226

Macromolecule Content

Total Structure Weight: 427.23 kDa
Atom Count: 23,442
Modeled Residue Count: 3,003
Deposited Residue Count: 3,864
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	A, B, C	1,288	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 7 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0DTC2
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.84 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	UCSF Chimera
MODEL REFINEMENT	PHENIX

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-20

Deposition Author(s):

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: 2022-07-20
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.2: 2024-10-23
Changes: Data collection, Structure summary
Version 1.3: 2025-05-14
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.