5ZVK | pdb_00005zvk

Crystal Structure of the Human Coronavirus MERS HR1 motif in complex with pan-CoVs inhibitor EK1

• PDB DOI: https://doi.org/10.2210/pdb5ZVK/pdb

• Classification: VIRAL PROTEIN/INHIBITOR
• Organism(s): Middle East respiratory syndrome-related coronavirus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-11 Released: 2019-04-10 
• Deposition Author(s): Yan, L., Yang, B., Wilson, I.A.
• Funding Organization(s): National Science Foundation (China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free: 
  0.314 (Depositor), 0.317 (DCC) 
• R-Value Work: 
  0.259 (Depositor), 0.263 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

Starting Model: experimental

Literature

A pan-coronavirus fusion inhibitor targeting the HR1 domain of human coronavirus spike.

Xia, S., Yan, L., Xu, W., Agrawal, A.S., Algaissi, A., Tseng, C.K., Wang, Q., Du, L., Tan, W., Wilson, I.A., Jiang, S., Yang, B., Lu, L.

(2019) Sci Adv 5: eaav4580-eaav4580

• PubMed: 30989115 
• DOI: https://doi.org/10.1126/sciadv.aav4580
• Primary Citation Related Structures: 
  5ZUV, 5ZVK, 5ZVM


• PubMed Abstract: 
  

  Continuously emerging highly pathogenic human coronaviruses (HCoVs) remain a major threat to human health, as illustrated in past SARS-CoV and MERS-CoV outbreaks. The development of a drug with broad-spectrum HCoV inhibitory activity would address this urgent unmet medical need. Although previous studies have suggested that the HR1 of HCoV spike (S) protein is an important target site for inhibition against specific HCoVs, whether this conserved region could serve as a target for the development of broad-spectrum pan-CoV inhibitor remains controversial. Here, we found that peptide OC43-HR2P, derived from the HR2 domain of HCoV-OC43, exhibited broad fusion inhibitory activity against multiple HCoVs. EK1, the optimized form of OC43-HR2P, showed substantially improved pan-CoV fusion inhibitory activity and pharmaceutical properties. Crystal structures indicated that EK1 can form a stable six-helix bundle structure with both short α-HCoV and long β-HCoV HR1s, further supporting the role of HR1 region as a viable pan-CoV target site.

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Organizational Affiliation: 
• Shanghai Public Health Clinical Center and School of Basic Medical Sciences, and Key Laboratory of Medical Molecular Virology of MOE/MOH, Fudan University, Shanghai 200032, China.
Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China.
Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
Department of Medical Laboratories Technology, College of Applied Medical Sciences, Jazan University, Jazan, Saudi Arabia.
Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY 10065, USA.
MOH Key Laboratory of Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
Department of Integrative Structural and Computational Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, BCC206, La Jolla, CA 92037, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A3B3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 40.46 kDa 
• Atom Count: 2,341 
• Modeled Residue Count: 301 
• Deposited Residue Count: 372 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Human Coronavirus MERS HR1 motif	A, B, C	80	Middle East respiratory syndrome-related coronavirus	Mutation(s): 0
UniProt
Find proteins for K9N5Q8 (Middle East respiratory syndrome-related coronavirus (isolate United Kingdom/H123990006/2012)) Explore K9N5Q8  Go to UniProtKB:  K9N5Q8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
pan-CoV inhibitory peptide EK1	D [auth a], E [auth b], F [auth c]	44	synthetic construct	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.31 Å
• R-Value Free:  0.314 (Depositor), 0.317 (DCC) 
• R-Value Work:  0.259 (Depositor), 0.263 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.28	α = 90
b = 60.28	β = 90
c = 175.228	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Yan, L., Yang, B., Wilson, I.A.

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Funding Organization	Location	Grant Number
National Science Foundation (China)	China	31600619

Revision History  

• Version 1.0: 2019-04-10
  Type: Initial release
  
• Version 1.1: 2019-04-17
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2019-05-15
  Changes: Data collection, Database references
• Version 1.3: 2019-08-28
  Changes: Data collection
• Version 1.4: 2023-11-22
  Changes: Data collection, Database references, Refinement description