3D0H

Crystal structure of spike protein receptor-binding domain from the 2002-2003 SARS coronavirus civet strain complexed with human-civet chimeric receptor ACE2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of major species barriers between humans and palm civets for severe acute respiratory syndrome coronavirus infections

Li, F.

(2008) J.Virol. 82: 6984-6991

  • DOI: 10.1128/JVI.00442-08
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • It is believed that a novel coronavirus, severe acute respiratory syndrome coronavirus (SARS-CoV), was passed from palm civets to humans and caused the epidemic of SARS in 2002 to 2003. The major species barriers between humans and civets for SARS-Co ...

    It is believed that a novel coronavirus, severe acute respiratory syndrome coronavirus (SARS-CoV), was passed from palm civets to humans and caused the epidemic of SARS in 2002 to 2003. The major species barriers between humans and civets for SARS-CoV infections are the specific interactions between a defined receptor-binding domain (RBD) on a viral spike protein and its host receptor, angiotensin-converting enzyme 2 (ACE2). In this study a chimeric ACE2 bearing the critical N-terminal helix from civet and the remaining peptidase domain from human was constructed, and it was shown that this construct has the same receptor activity as civet ACE2. In addition, crystal structures of the chimeric ACE2 complexed with RBDs from various human and civet SARS-CoV strains were determined. These structures, combined with a previously determined structure of human ACE2 complexed with the RBD from a human SARS-CoV strain, have revealed a structural basis for understanding the major species barriers between humans and civets for SARS-CoV infections. They show that the major species barriers are determined by interactions between four ACE2 residues (residues 31, 35, 38, and 353) and two RBD residues (residues 479 and 487), that early civet SARS-CoV isolates were prevented from infecting human cells due to imbalanced salt bridges at the hydrophobic virus/receptor interface, and that SARS-CoV has evolved to gain sustained infectivity for human cells by eliminating unfavorable free charges at the interface through stepwise mutations at positions 479 and 487. These results enhance our understanding of host adaptations and cross-species infections of SARS-CoV and other emerging animal viruses.


    Organizational Affiliation

    Department of Pharmacology, University of Minnesota Medical School, 6-121 Jackson Hall, 321 Church St. S.E., Minneapolis, MN 55455, USA. lifang@umn.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Angiotensin-converting enzyme 2
A, B
597Homo sapiensPaguma larvata
This entity is chimeric
Mutation(s): 0 
Gene Names: ACE2, ACE2
EC: 3.4.17.23 3.4.17.23
Find proteins for Q9BYF1 (Homo sapiens)
Go to Gene View: ACE2
Go to UniProtKB:  Q9BYF1
Find proteins for Q56NL1 (Paguma larvata)
Go to Gene View: ACE2
Go to UniProtKB:  Q56NL1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Spike glycoprotein
E, F
179Human SARS coronavirusMutation(s): 0 
Gene Names: S
Find proteins for P59594 (Human SARS coronavirus)
Go to UniProtKB:  P59594
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NDG
Query on NDG

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Download CCD File 
A, B, F
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.221 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.352α = 90.00
b = 119.841β = 95.89
c = 109.420γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2008-05-01 
  • Released Date: 2008-07-08 
  • Deposition Author(s): Li, F.

Revision History 

  • Version 1.0: 2008-07-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-06-14
    Type: Database references, Source and taxonomy, Structure summary