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 
  • R-Value Work: 0.268 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 106: 19970-19974

  • DOI: 10.1073/pnas.0908837106

  • 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 investi ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Angiotensin-converting enzyme 2
A, B, C, D
597Homo sapiensMutation(s): 0 
Gene Names: ACE2
EC: 3.4.17.23
Find proteins for Q9BYF1 (Homo sapiens)
Go to Gene View: ACE2
Go to UniProtKB:  Q9BYF1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Spike glycoprotein
E, F, G, H
136Human coronavirus NL63Mutation(s): 0 
Gene Names: S
Find proteins for Q6Q1S2 (Human coronavirus NL63)
Go to UniProtKB:  Q6Q1S2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.31 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.268 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 77.764α = 90.00
b = 77.764β = 90.00
c = 631.095γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-3000data scaling
REFMACrefinement
HKL-3000data reduction
HKL-3000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2018-04-18
    Type: Data collection