6ATK

Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.505 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Receptor-binding loops in alphacoronavirus adaptation and evolution.

Wong, A.H.M.Tomlinson, A.C.A.Zhou, D.Satkunarajah, M.Chen, K.Sharon, C.Desforges, M.Talbot, P.J.Rini, J.M.

(2017) Nat Commun 8: 1735-1735

  • DOI: 10.1038/s41467-017-01706-x

  • PubMed Abstract: 
  • RNA viruses are characterized by a high mutation rate, a buffer against environmental change. Nevertheless, the means by which random mutation improves viral fitness is not well characterized. Here we report the X-ray crystal structure of the recepto ...

    RNA viruses are characterized by a high mutation rate, a buffer against environmental change. Nevertheless, the means by which random mutation improves viral fitness is not well characterized. Here we report the X-ray crystal structure of the receptor-binding domain (RBD) of the human coronavirus, HCoV-229E, in complex with the ectodomain of its receptor, aminopeptidase N (APN). Three extended loops are solely responsible for receptor binding and the evolution of HCoV-229E and its close relatives is accompanied by changing loop-receptor interactions. Phylogenetic analysis shows that the natural HCoV-229E receptor-binding loop variation observed defines six RBD classes whose viruses have successively replaced each other in the human population over the past 50 years. These RBD classes differ in their affinity for APN and their ability to bind an HCoV-229E neutralizing antibody. Together, our results provide a model for alphacoronavirus adaptation and evolution based on the use of extended loops for receptor binding.


    Organizational Affiliation

    Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminopeptidase N
A, B, C
905Homo sapiensMutation(s): 0 
Gene Names: ANPEP (APN, CD13, PEPN)
EC: 3.4.11.2
Find proteins for P15144 (Homo sapiens)
Go to Gene View: ANPEP
Go to UniProtKB:  P15144
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Spike glycoprotein
E, D, F
146Human coronavirus 229EMutation(s): 0 
Gene Names: S
Find proteins for P15423 (Human coronavirus 229E)
Go to UniProtKB:  P15423
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.505 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.244 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 153.820α = 90.00
b = 153.820β = 90.00
c = 322.120γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-08-29 
  • Released Date: 2017-12-06 
  • Deposition Author(s): Wong, A.H., Rini, J.M.

Funding OrganizationLocationGrant Number
Canadian Institutes of Health ResearchCanada--

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release