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 8ZY6 | pdb_00008zy6

Sarbecovirus GX2013 Spike Trimer in a Locked Conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8ZY6

This is version 1.4 of the entry. See complete history. 

Literature

SARS-related coronavirus S-protein structures reveal synergistic RBM interactions underpinning high-affinity human ACE2 binding.

Wang, J., Ma, Y., Li, Z., Yuan, H., Liu, B., Li, Z., Su, M., Habib, G., Liu, Y., Fu, L., Wang, P., Li, M., He, J., Chen, J., Zhou, P., Shi, Z., Chen, X., Xiong, X.

(2025) Sci Adv 11: eadr8772-eadr8772

  • DOI: https://doi.org/10.1126/sciadv.adr8772
  • Primary Citation Related Structures: 
    8ZY0, 8ZY1, 8ZY2, 8ZY3, 8ZY4, 8ZY5, 8ZY6, 8ZY7, 8ZY9, 8ZYA

  • PubMed Abstract: 

    High-affinity and specific binding toward the human angiotensin-converting enzyme 2 (hACE2) receptor by severe acute respiratory syndrome coronavirus (SARS)-related coronaviruses (SARSr-CoVs) remains incompletely understood. We report cryo-electron microscopy structures of eight different S-proteins from SARSr-CoVs found across Asia, Europe, and Africa. These S-proteins all adopt tightly packed, locked, prefusion conformations. These structures enable the classification of SARSr-CoV S-proteins into three types, based on their receptor-binding motif (RBM) structures and ACE2 binding characteristics. Type-2 S-proteins often preferentially bind bat ACE2 (bACE2) over hACE2. We report a structure of a type-2 BtKY72-RBD in complex with bACE2 to understand ACE2 specificity. Structure-guided mutagenesis of BtKY72-RBD reveals that multiple synergistic mutations in four different regions of RBM are required to achieve high-affinity hACE2 binding. Similar RBM changes can also confer hACE2 binding to another type-2 BM48-31 S-protein, which is primarily non-ACE2 binding. These results provide an understanding of how high-affinity hACE2 binding may be acquired by SARSr-CoV S-proteins.


  • Organizational Affiliation: 
    • Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangdong-Hong Kong Joint Research Laboratory for Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.

Macromolecule Content 

  • Total Structure Weight: 431.07 kDa 
  • Atom Count: 25,275 
  • Modeled Residue Count: 3,123 
  • Deposited Residue Count: 3,768 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Spike glycoproteinA [auth C],
B [auth A],
C [auth B]
1,256BtRs-BetaCoV/GX2013Mutation(s): 0 
UniProt
Find proteins for A0A0U1WHJ8 (BtRs-BetaCoV/GX2013)
Explore A0A0U1WHJ8 
Go to UniProtKB:  A0A0U1WHJ8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U1WHJ8
Glycosylation
Glycosylation Sites: 10
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F, G, H
D, E, F, G, H, I, J, K, L, M, N, O
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
(Subject of Investigation/LOI)

Query on NAG



Download:Ideal Coordinates CCD File
AA [auth C]
AB [auth B]
BA [auth C]
BB [auth B]
CA [auth C]
AA [auth C],
AB [auth B],
BA [auth C],
BB [auth B],
CA [auth C],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
HA [auth A],
IA [auth A],
JA [auth A],
KA [auth A],
LA [auth A],
MA [auth A],
NA [auth A],
OA [auth A],
P [auth C],
PA [auth A],
Q [auth C],
QA [auth B],
R [auth C],
RA [auth B],
S [auth C],
SA [auth B],
T [auth C],
TA [auth B],
U [auth C],
UA [auth B],
V [auth C],
VA [auth B],
W [auth C],
WA [auth B],
X [auth C],
XA [auth B],
Y [auth C],
YA [auth B],
Z [auth C],
ZA [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: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government2022A1515110495
Other governmentSRPG22-002

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-02-26
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-06-18
    Changes: Data collection, Database references
  • Version 1.4: 2025-07-16
    Changes: Data collection