6VW1

Structure of SARS-CoV-2 chimeric receptor-binding domain complexed with its receptor human ACE2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Structural basis of receptor recognition by SARS-CoV-2.

Shang, J.Ye, G.Shi, K.Wan, Y.Luo, C.Aihara, H.Geng, Q.Auerbach, A.Li, F.

(2020) Nature 581: 221-224

  • DOI: 10.1038/s41586-020-2179-y
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A novel SARS-like coronavirus (SARS-CoV-2) recently emerged and is rapidly spreading in humans 1,2 . A key to tackling this epidemic is to understand the virus's receptor recognition mechanism, which regulates its infectivity, pathogenesis ...

    A novel SARS-like coronavirus (SARS-CoV-2) recently emerged and is rapidly spreading in humans 1,2 . A key to tackling this epidemic is to understand the virus's receptor recognition mechanism, which regulates its infectivity, pathogenesis and host range. SARS-CoV-2 and SARS-CoV recognize the same receptor - human ACE2 (hACE2) 3,4 . Here we determined the crystal structure of the SARS-CoV-2 receptor-binding domain (RBD) (engineered to facilitate crystallization) in complex with hACE2. Compared with the SARS-CoV RBD, a hACE2-binding ridge in SARS-CoV-2 RBD takes a more compact conformation; moreover, several residue changes in SARS-CoV-2 RBD stabilize two virus-binding hotspots at the RBD/hACE2 interface. These structural features of SARS-CoV-2 RBD enhance its hACE2-binding affinity. Additionally, we show that RaTG13, a bat coronavirus closely related to SARS-CoV-2, also uses hACE2 as its receptor. The differences among SARS-CoV-2, SARS-CoV and RaTG13 in hACE2 recognition shed light on potential animal-to-human transmission of SARS-CoV-2. This study provides guidance for intervention strategies targeting receptor recognition by SARS-CoV-2.


    Organizational Affiliation

    Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN, USA. lifang@umn.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Angiotensin-converting enzyme 2
A, B
597Homo 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
SARS-CoV-2 chimeric RBD
E, F
217Severe acute respiratory syndrome-related coronavirusSevere acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
Find proteins for P59594 (Human SARS coronavirus)
Go to UniProtKB:  P59594
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Go to UniProtKB:  P0DTC2
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

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

Download CCD File 
A, B, E
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A, B
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.435α = 90
b = 118.034β = 93.12
c = 112.075γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01AI089728
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01AI089728
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM118047

Revision History 

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-03-11
    Changes: Source and taxonomy
  • Version 1.2: 2020-04-08
    Changes: Database references, Structure summary
  • Version 1.3: 2020-04-15
    Changes: Database references, Structure summary
  • Version 1.4: 2020-05-06
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 1.5: 2020-05-27
    Changes: Database references