5X59 | pdb_00005x59

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

• PDB DOI: https://doi.org/10.2210/pdb5X59/pdb
• EM Map EMD-6704: EMDB EMDataResource

• Classification: VIRAL PROTEIN
• Organism(s): Middle East respiratory syndrome-related coronavirus
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2017-02-15 Released: 2017-05-03 
• Deposition Author(s): 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.

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Experimental Data Snapshot

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

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

• PubMed: 28393837 
• DOI: https://doi.org/10.1038/ncomms15092
• Primary Citation 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.

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Organizational Affiliation: 
• School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.
CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
Laboratory of Protein Engineering and Vaccines, Tianjin Institute of Biotechnology, Tianjin 300308, China.
CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.
West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan 610041, China.
School of Basic Medical Sciences, Wuhan University, Wuhan 430071, China.
Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China.
Center for Influenza Research and Early-warning, Chinese Academy of Sciences (CASCIRE), Beijing 100101, China.
Medical School, University of Chinese Academy of Sciences, Beijing 101408, China.
Center for Biological Imaging, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 444.2 kDa 
• Atom Count: 26,838 
• Modeled Residue Count: 3,423 
• Deposited Residue Count: 3,969 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S protein	A, B, C	1,323	Middle East respiratory syndrome-related coronavirus	Mutation(s): 2
UniProt
Find proteins for K9N5Q8 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N5Q8  Go to UniProtKB:  K9N5Q8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	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 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): 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.

Revision History  

• 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
• Version 1.5: 2025-07-02
  Changes: Data collection