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: 3.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 

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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: https://doi.org/10.1038/s41467-017-01706-x
  • Primary Citation of Related Structures:  
    6ATK

  • 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 receptor-binding domain (RBD) of the human coronavirus, HCoV-229E, in complex with the ectodomain of its receptor, aminopeptidase N (APN) ...

    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 Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada, M5S 1A8. james.rini@utoronto.ca.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aminopeptidase N
A, B, C
905Homo sapiensMutation(s): 0 
Gene Names: ANPEP, APN, CD13, PEPN
EC: 3.4.11.2
UniProt & NIH Common Fund Data Resources
Find proteins for P15144 (Homo sapiens)
Explore P15144 
Go to UniProtKB:  P15144
PHAROS:  P15144
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15144
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinD [auth E],
E [auth D],
F		146Human coronavirus 229EMutation(s): 0 
Gene Names: S, 2
UniProt
Find proteins for P15423 (Human coronavirus 229E)
Explore P15423 
Go to UniProtKB:  P15423
Entity Groups  
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UniProt GroupP15423
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J, K
2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
AA [auth E]
BA [auth E]
CA [auth D]
L [auth A]
M [auth A]
AA [auth E],
BA [auth E],
CA [auth D],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
Q [auth A],
R [auth B],
S [auth B],
T [auth B],
V [auth C],
W [auth C],
X [auth C],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
P [auth A],
U [auth B],
Y [auth C]		ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.245 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 153.82α = 90
b = 153.82β = 90
c = 322.12γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada--

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2020-01-08
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary