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 
  • R-Value Observed: 0.270 

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This is version 1.3 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinB [auth E], D [auth F], F [auth G], H136Human 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
I [auth A] , J [auth A] , K [auth E] , L [auth E] , M [auth B] , N [auth B] , O [auth F] , P [auth F] , 
I [auth A],  J [auth A],  K [auth E],  L [auth E],  M [auth B],  N [auth B],  O [auth F],  P [auth F],  Q [auth C],  R [auth C],  S [auth G],  T [auth G],  U [auth D],  V [auth D],  W [auth H],  X [auth H]
2-acetamido-2-deoxy-beta-D-glucopyranose
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 
  • R-Value Observed: 0.270 
  • 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

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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