6LZG

Structure of novel coronavirus spike receptor-binding domain complexed with its receptor ACE2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.5 of the entry. See complete history


Literature

Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2.

Wang, Q.Zhang, Y.Wu, L.Niu, S.Song, C.Zhang, Z.Lu, G.Qiao, C.Hu, Y.Yuen, K.Y.Wang, Q.Zhou, H.Yan, J.Qi, J.

(2020) Cell 181: 894-904.e9

  • DOI: https://doi.org/10.1016/j.cell.2020.03.045
  • Primary Citation of Related Structures:  
    6LZG

  • PubMed Abstract: 

    The recent emergence of a novel coronavirus (SARS-CoV-2) in China has caused significant public health concerns. Recently, ACE2 was reported as an entry receptor for SARS-CoV-2. In this study, we present the crystal structure of the C-terminal domain of SARS-CoV-2 (SARS-CoV-2-CTD) spike (S) protein in complex with human ACE2 (hACE2), which reveals a hACE2-binding mode similar overall to that observed for SARS-CoV. However, atomic details at the binding interface demonstrate that key residue substitutions in SARS-CoV-2-CTD slightly strengthen the interaction and lead to higher affinity for receptor binding than SARS-RBD. Additionally, a panel of murine monoclonal antibodies (mAbs) and polyclonal antibodies (pAbs) against SARS-CoV-S1/receptor-binding domain (RBD) were unable to interact with the SARS-CoV-2 S protein, indicating notable differences in antigenicity between SARS-CoV and SARS-CoV-2. These findings shed light on the viral pathogenesis and provide important structural information regarding development of therapeutic countermeasures against the emerging virus.


  • Organizational Affiliation

    CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Shenzhen Key Laboratory of Pathogen and Immunity, Shenzhen Third People's Hospital, Shenzhen 518112, China; CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2596Homo sapiensMutation(s): 0 
Gene Names: ACE2UNQ868/PRO1885
EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)
Explore Q9BYF1 
Go to UniProtKB:  Q9BYF1
GTEx:  ENSG00000130234 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BYF1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Spike protein S1209Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S2
Membrane Entity: Yes 
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTC2
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.448α = 90
b = 104.448β = 90
c = 229.786γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data processing
PHASERphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-18
    Type: Initial release
  • Version 1.1: 2020-04-08
    Changes: Structure summary
  • Version 2.0: 2020-04-22
    Type: Coordinate replacement
    Reason: Model orientation/position
    Changes: Advisory, Atomic model, Author supporting evidence, Database references, Polymer sequence, Refinement description, Source and taxonomy, Structure summary
  • Version 2.1: 2020-05-06
    Changes: Database references, Source and taxonomy, Structure summary
  • Version 2.2: 2020-05-27
    Changes: Database references
  • Version 2.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 2.4: 2021-03-10
    Changes: Structure summary
  • Version 2.5: 2023-11-29
    Changes: Data collection, Database references, Refinement description