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 7MTC | pdb_00007mtc

Structure of freshly purified SARS-CoV-2 S2P spike at pH 7.4


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7MTC

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

Literature

SARS-CoV-2 S2P spike ages through distinct states with altered immunogenicity.

Olia, A.S., Tsybovsky, Y., Chen, S.J., Liu, C., Nazzari, A.F., Ou, L., Wang, L., Kong, W.P., Leung, K., Liu, T., Stephens, T., Teng, I.T., Wang, S., Yang, E.S., Zhang, B., Zhang, Y., Zhou, T., Mascola, J.R., Kwong, P.D.

(2021) J Biol Chem 297: 101127-101127

  • DOI: https://doi.org/10.1016/j.jbc.2021.101127
  • Primary Citation Related Structures: 
    7MTC, 7MTD, 7MTE

  • PubMed Abstract: 

    The SARS-CoV-2 spike is the primary target of virus-neutralizing antibodies and critical to the development of effective vaccines against COVID-19. Here, we demonstrate that the prefusion-stabilized two-proline "S2P" spike-widely employed for laboratory work and clinical studies-unfolds when stored at 4 °C, physiological pH, as observed by electron microscopy (EM) and differential scanning calorimetry, but that its trimeric, native-like conformation can be reacquired by low pH treatment. When stored for approximately 1 week, this unfolding does not significantly alter antigenic characteristics; however, longer storage diminishes antibody binding, and month-old spike elicits virtually no neutralization in mice despite inducing high ELISA-binding titers. Cryo-EM structures reveal the folded fraction of spike to decrease with aging; however, its structure remains largely similar, although with varying mobility of the receptor-binding domain. Thus, the SARS-CoV-2 spike is susceptible to unfolding, which affects immunogenicity, highlighting the need to monitor its integrity.


  • Organizational Affiliation: 
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA.

Macromolecule Content 

  • Total Structure Weight: 433.64 kDa 
  • Atom Count: 21,178 
  • Modeled Residue Count: 2,642 
  • Deposited Residue Count: 3,843 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,281Severe acute respiratory syndrome coronavirus 2Mutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Glycosylation
Glycosylation Sites: 8Go to GlyGen: P0DTC2-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth B]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth B],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth B],
W [auth B],
X [auth B],
Y [auth B],
Z [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: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2021-10-13
    Changes: Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-05-14
    Changes: Data collection