5X59

Prefusion structure of MERS-CoV spike glycoprotein, three-fold symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains

Yuan, Y.Cao, D.Zhang, Y.Ma, J.Qi, J.Wang, Q.Lu, G.Wu, Y.Yan, J.Shi, Y.Zhang, X.Gao, G.F.

(2017) Nat Commun 8: 15092-15092

  • DOI: https://doi.org/10.1038/ncomms15092
  • Primary Citation of Related Structures:  
    5X4R, 5X4S, 5X58, 5X59, 5X5B, 5X5C, 5X5F

  • PubMed Abstract: 

    The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. Here, we present high-resolution structures of the trimeric MERS-CoV and SARS-CoV S proteins in its pre-fusion conformation by single particle cryo-electron microscopy. The overall structures resemble that from other coronaviruses including HKU1, MHV and NL63 reported recently, with the exception of the receptor binding domain (RBD). We captured two states of the RBD with receptor binding region either buried (lying state) or exposed (standing state), demonstrating an inherently flexible RBD readily recognized by the receptor. Further sequence conservation analysis of six human-infecting coronaviruses revealed that the fusion peptide, HR1 region and the central helix are potential targets for eliciting broadly neutralizing antibodies.


  • Organizational Affiliation

    School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
S protein
A, B, C
1,323Middle East respiratory syndrome-related coronavirusMutation(s): 2 
UniProt
Find proteins for K9N5Q8 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012))
Explore K9N5Q8 
Go to UniProtKB:  K9N5Q8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupK9N5Q8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
D [auth A]
DA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
D [auth A],
DA [auth C],
E [auth A],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
GA [auth C],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth C],
Y [auth C],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-24
    Changes: Refinement description
  • Version 1.2: 2019-10-16
    Changes: Data collection, Other
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-10-30
    Changes: Data collection, Database references, Structure summary