7WBP

Crystal structure of the receptor binding domain of SARS-CoV-2 Omicron variant spike glycoprotein in complex with its receptor human ACE2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

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Literature

Receptor binding and complex structures of human ACE2 to spike RBD from omicron and delta SARS-CoV-2.

Han, P.Li, L.Liu, S.Wang, Q.Zhang, D.Xu, Z.Han, P.Li, X.Peng, Q.Su, C.Huang, B.Li, D.Zhang, R.Tian, M.Fu, L.Gao, Y.Zhao, X.Liu, K.Qi, J.Gao, G.F.Wang, P.

(2022) Cell 185: 630-640.e10

  • DOI: 10.1016/j.cell.2022.01.001
  • Primary Citation of Related Structures:  
    7WBL, 7WBP, 7WBQ

  • PubMed Abstract: 
  • The coronavirus disease 2019 (COVID-19) pandemic continues worldwide with many variants arising, some of which are variants of concern (VOCs). A recent VOC, omicron (B.1.1.529), which obtains a large number of mutations in the receptor-binding domain (RBD) of the spike protein, has risen to intense scientific and public attention ...

    The coronavirus disease 2019 (COVID-19) pandemic continues worldwide with many variants arising, some of which are variants of concern (VOCs). A recent VOC, omicron (B.1.1.529), which obtains a large number of mutations in the receptor-binding domain (RBD) of the spike protein, has risen to intense scientific and public attention. Here, we studied the binding properties between the human receptor ACE2 (hACE2) and the VOC RBDs and resolved the crystal and cryoelectron microscopy structures of the omicron RBD-hACE2 complex as well as the crystal structure of the delta RBD-hACE2 complex. We found that, unlike alpha, beta, and gamma, omicron RBD binds to hACE2 at a similar affinity to that of the prototype RBD, which might be due to compensation of multiple mutations for both immune escape and transmissibility. The complex structures of omicron RBD-hACE2 and delta RBD-hACE2 reveal the structural basis of how RBD-specific mutations bind to hACE2.


    Organizational Affiliation

    Cryo-EM Center, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China. Electronic address: wangpy@sustech.edu.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Angiotensin-converting enzyme 2A596Homo sapiensMutation(s): 0 
Gene Names: ACE2UNQ868/PRO1885
EC: 3.4.17.23 (PDB Primary Data), 3.4.17 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYF1 (Homo sapiens)
Explore Q9BYF1 
Go to UniProtKB:  Q9BYF1
PHAROS:  Q9BYF1
Entity Groups  
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UniProt GroupQ9BYF1
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Spike protein S1B223Severe acute respiratory syndrome coronavirus 2Mutation(s): 15 
Gene Names: S2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC2 
Go to UniProtKB:  P0DTC2
Entity Groups  
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UniProt GroupP0DTC2
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseC 2N-Glycosylation Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.238α = 90
b = 104.238β = 90
c = 227.178γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-12-17 
  • Released Date: 2022-01-19 
  • Deposition Author(s): Qi, J., Han, P.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2022-03-02
    Changes: Database references