7TLZ

SARS-CoV-2 S NTD B.1.1.529 Omicron variant + S309 Local Refinement


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement.

McCallum, M.Czudnochowski, N.Rosen, L.E.Zepeda, S.K.Bowen, J.E.Walls, A.C.Hauser, K.Joshi, A.Stewart, C.Dillen, J.R.Powell, A.E.Croll, T.I.Nix, J.Virgin, H.W.Corti, D.Snell, G.Veesler, D.

(2022) Science 375: 864-868

  • DOI: 10.1126/science.abn8652
  • Primary Citation of Related Structures:  
    7TLY, 7TLZ, 7TM0, 7TN0

  • PubMed Abstract: 
  • The SARS-CoV-2 Omicron variant of concern evades antibody-mediated immunity that comes from vaccination or infection with earlier variants due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo-electron microscopy and X-ray crystal structures of the spike protein and the receptor-binding domain bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor ...

    The SARS-CoV-2 Omicron variant of concern evades antibody-mediated immunity that comes from vaccination or infection with earlier variants due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo-electron microscopy and X-ray crystal structures of the spike protein and the receptor-binding domain bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor. We provide a blueprint for understanding the marked reduction of binding of other therapeutic mAbs that leads to dampened neutralizing activity. Remodeling of interactions between the Omicron receptor-binding domain and human ACE2 likely explains the enhanced affinity for the host receptor relative to the ancestral virus.


    Organizational Affiliation

    Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
S2L20 Fab light chainA107Homo sapiensMutation(s): 0 
Entity Groups  
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Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
S2L20 Fab heavy chainB122Homo sapiensMutation(s): 0 
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Protein Feature View
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinC [auth J]1274Homo sapiensMutation(s): 40 
Gene Names: S2
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
D [auth J],
E [auth J],
F [auth J],
G [auth J],
H [auth J],
D [auth J],
E [auth J],
F [auth J],
G [auth J],
H [auth J],
I [auth J]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-02
    Type: Initial release
  • Version 1.1: 2022-02-09
    Changes: Database references
  • Version 1.2: 2022-03-09
    Changes: Database references