5KWB

Crystal Structure of the Receptor Binding Domain of the Spike Glycoprotein of Human Betacoronavirus HKU1 (HKU1 1A-CTD, 1.9 angstrom, molecular replacement)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the receptor binding domain of the spike glycoprotein of human betacoronavirus HKU1

Ou, X.Guan, H.Qin, B.Mu, Z.Wojdyla, J.A.Wang, M.Dominguez, S.R.Qian, Z.Cui, S.

(2017) Nat Commun 8: 15216-15216

  • DOI: 10.1038/ncomms15216
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human coronavirus (CoV) HKU1 is a pathogen causing acute respiratory illnesses and so far little is known about its biology. HKU1 virus uses its S1 subunit C-terminal domain (CTD) and not the N-terminal domain like other lineage A β-CoVs to bind to i ...

    Human coronavirus (CoV) HKU1 is a pathogen causing acute respiratory illnesses and so far little is known about its biology. HKU1 virus uses its S1 subunit C-terminal domain (CTD) and not the N-terminal domain like other lineage A β-CoVs to bind to its yet unknown human receptor. Here we present the crystal structure of HKU1 CTD at 1.9 Å resolution. The structure consists of three subdomains: core, insertion and subdomain-1 (SD-1). While the structure of the core and SD-1 subdomains of HKU1 are highly similar to those of other β-CoVs, the insertion subdomain adopts a novel fold, which is largely invisible in the cryo-EM structure of the HKU1 S trimer. We identify five residues in the insertion subdomain that are critical for binding of neutralizing antibodies and two residues essential for receptor binding. Our study contributes to a better understanding of entry, immunity and evolution of CoV S proteins.


    Organizational Affiliation

    MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.,Swiss Light Source at Paul Scherrer Institute, Villigen CH-5232, Switzerland.,Departments of Pediatrics, University of Colorado School of Medicine, Aurora, Colorado 80045, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Spike glycoprotein
A
371Human coronavirus HKU1 (isolate N1)Mutation(s): 0 
Gene Names: S
Find proteins for Q5MQD0 (Human coronavirus HKU1 (isolate N1))
Go to UniProtKB:  Q5MQD0
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SUC
Query on SUC

Download SDF File 
Download CCD File 
A
SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.175 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 86.556α = 90.00
b = 183.800β = 90.00
c = 63.342γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
Cootmodel building
PHENIXrefinement
XDSdata processing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-06-14
    Type: Structure summary