Structure of SARS-CoV-1 Spike Protein with Engineered x1 Disulfide (S370C and D967C), Closed Conformation

Experimental Data Snapshot

  • Resolution: 2.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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Disulfide stabilization reveals conserved dynamic features between SARS-CoV-1 and SARS-CoV-2 spikes.

Zhang, X.Li, Z.Zhang, Y.Liu, Y.Wang, J.Liu, B.Chen, Q.Wang, Q.Fu, L.Wang, P.Zhong, X.Jin, L.Yan, Q.Chen, L.He, J.Zhao, J.Xiong, X.

(2023) Life Sci Alliance 6

  • DOI: https://doi.org/10.26508/lsa.202201796
  • Primary Citation of Related Structures:  
    8H0X, 8H0Y, 8H0Z, 8H10, 8H11, 8H12, 8H13, 8H14, 8H15, 8H16

  • PubMed Abstract: 

    SARS-CoV-2 spike protein (S) is structurally dynamic and has been observed by cryo-EM to adopt a variety of prefusion conformations that can be categorized as locked, closed, and open. S-trimers adopting locked conformations are tightly packed featuring structural elements incompatible with RBD in the "up" position. For SARS-CoV-2 S, it has been shown that the locked conformations are transient under neutral pH. Probably because of their transience, locked conformations remain largely uncharacterized for SARS-CoV-1 S. In this study, we introduced x1, x2, and x3 disulfides into SARS-CoV-1 S. Some of these disulfides have been shown to preserve rare locked conformations when introduced to SARS-CoV-2 S. Introduction of these disulfides allowed us to image a variety of locked and other rare conformations for SARS-CoV-1 S by cryo-EM. We identified bound cofactors and structural features that are associated with SARS-CoV-1 S locked conformations. We compare newly determined structures with other available spike structures of SARS-related CoVs to identify conserved features and discuss their possible functions.

  • Organizational Affiliation

    State Key Laboratory of Respiratory Disease, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinA [auth B],
B [auth A],
1,232Severe acute respiratory syndrome coronavirusMutation(s): 2 
Gene Names: S2
Find proteins for P59594 (Severe acute respiratory syndrome coronavirus)
Explore P59594 
Go to UniProtKB:  P59594
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP59594
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth C]
E [auth B]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth C],
E [auth B],
EA [auth C],
F [auth B],
FA [auth C],
G [auth B],
GA [auth C],
H [auth B],
HA [auth C],
I [auth B],
IA [auth C],
J [auth B],
JA [auth C],
K [auth B],
KA [auth C],
L [auth B],
LA [auth C],
M [auth B],
MA [auth C],
N [auth B],
NA [auth C],
O [auth B],
OA [auth C],
P [auth B],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
C8 H15 N O6
Experimental Data & Validation

Experimental Data

  • Resolution: 2.72 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2023-07-19
    Changes: Database references, Refinement description