3KBH

Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 
    0.300 (Depositor), 0.289 (DCC) 
  • R-Value Work: 
    0.268 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 
    0.270 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.4 of the entry. See complete history


Literature

Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor.

Wu, K.Li, W.Peng, G.Li, F.

(2009) Proc Natl Acad Sci U S A 106: 19970-19974

  • DOI: https://doi.org/10.1073/pnas.0908837106
  • Primary Citation of Related Structures:  
    3KBH

  • PubMed Abstract: 

    NL63 coronavirus (NL63-CoV), a prevalent human respiratory virus, is the only group I coronavirus known to use angiotensin-converting enzyme 2 (ACE2) as its receptor. Incidentally, ACE2 is also used by group II SARS coronavirus (SARS-CoV). We investigated how different groups of coronaviruses recognize the same receptor, whereas homologous group I coronaviruses recognize different receptors. We determined the crystal structure of NL63-CoV spike protein receptor-binding domain (RBD) complexed with human ACE2. NL63-CoV RBD has a novel beta-sandwich core structure consisting of 2 layers of beta-sheets, presenting 3 discontinuous receptor-binding motifs (RBMs) to bind ACE2. NL63-CoV and SARS-CoV have no structural homology in RBD cores or RBMs; yet the 2 viruses recognize common ACE2 regions, largely because of a "virus-binding hotspot" on ACE2. Among group I coronaviruses, RBD cores are conserved but RBMs are variable, explaining how these viruses recognize different receptors. These results provide a structural basis for understanding viral evolution and virus-receptor interactions.


  • Organizational Affiliation

    Department of Pharmacology, University of Minnesota Medical School, Minneapolis, MN 55455, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2A,
C [auth B],
E [auth C],
G [auth D]
597Homo sapiensMutation(s): 0 
Gene Names: ACE2spike proteinUNQ868/PRO1885
EC: 3.4.17 (PDB Primary Data), 3.4.17.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)
Explore Q9BYF1 
Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1
GTEx:  ENSG00000130234 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYF1
Glycosylation
Glycosylation Sites: 2Go to GlyGen: Q9BYF1-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoproteinB [auth E],
D [auth F],
F [auth G],
H
136Human coronavirus NL63Mutation(s): 0 
Gene Names: 2human angiotensin-converting enzyme 2S
UniProt
Find proteins for Q6Q1S2 (Human coronavirus NL63)
Explore Q6Q1S2 
Go to UniProtKB:  Q6Q1S2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6Q1S2
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A]
J [auth A]
K [auth E]
L [auth E]
M [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free:  0.300 (Depositor), 0.289 (DCC) 
  • R-Value Work:  0.268 (Depositor), 0.263 (DCC) 
  • R-Value Observed: 0.270 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.764α = 90
b = 77.764β = 90
c = 631.095γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
AMoREphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NAGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2018-04-18
    Changes: Data collection
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary
  • Version 1.4: 2024-11-27
    Changes: Data collection, Database references, Structure summary