6M0J

Crystal structure of SARS-CoV-2 spike receptor-binding domain bound with ACE2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.

Lan, J.Ge, J.Yu, J.Shan, S.Zhou, H.Fan, S.Zhang, Q.Shi, X.Wang, Q.Zhang, L.Wang, X.

(2020) Nature 

  • DOI: 10.1038/s41586-020-2180-5
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A new and highly pathogenic coronavirus (severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)) caused an outbreak in Wuhan city, Hubei province, China starting from December 2019 that quickly spread nationwide and to other countries around th ...

    A new and highly pathogenic coronavirus (severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)) caused an outbreak in Wuhan city, Hubei province, China starting from December 2019 that quickly spread nationwide and to other countries around the world 1-3 . Here, to better understand the initial step of infection at an atomic level, we determined the crystal structure of the receptor-binding domain (RBD) of the spike protein of SARS-CoV-2 bound to the cell receptor ACE2. The overall ACE2-binding mode of the SARS-CoV-2 RBD is nearly identical to that of the SARS-CoV RBD, which also uses ACE2 as the cell receptor 4 . Structural analysis identified residues in the SARS-CoV-2 RBD that are essential for ACE2 binding, the majority of which either are highly conserved or share similar side chain properties with those in the SARS-CoV RBD. Such similarity in structure and sequence strongly indicate convergent evolution between the SARS-CoV-2 and SARS-CoV RBDs for improved binding to ACE2, although SARS-CoV-2 does not cluster within SARS and SARS-related coronaviruses 1-3,5 . The epitopes of two SARS-CoV antibodies that target the RBD are also analysed for binding to the SARS-CoV-2 RBD, providing insights into the future identification of cross-reactive antibodies.


    Organizational Affiliation

    The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing, China. xinquanwang@mail.tsinghua.edu.cn.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Angiotensin-converting enzyme 2
A
603Homo sapiensMutation(s): 0 
Gene Names: ACE2UNQ868/PRO1885
EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
Find proteins for Q9BYF1 (Homo sapiens)
Go to UniProtKB:  Q9BYF1
NIH Common Fund Data Resources
PHAROS  Q9BYF1

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Spike receptor binding domain
E
229Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Go to UniProtKB:  P0DTC2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download CCD File 
A, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.67α = 90
b = 104.67β = 90
c = 228.72γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 2.0: 2020-04-08
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2020-04-15
    Changes: Database references
  • Version 2.2: 2020-05-06
    Changes: Database references, Source and taxonomy, Structure summary