7WLZ

Cryo-EM structure of the Omicron S in complex with 35B5 Fab(1 down-, 1 up- and 1 invisible RBDs)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 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

35B5 antibody potently neutralizes SARS-CoV-2 Omicron by disrupting the N-glycan switch via a conserved spike epitope.

Wang, X.Chen, X.Tan, J.Yue, S.Zhou, R.Xu, Y.Lin, Y.Yang, Y.Zhou, Y.Deng, K.Chen, Z.Ye, L.Zhu, Y.

(2022) Cell Host Microbe 30: 887

  • DOI: https://doi.org/10.1016/j.chom.2022.03.035
  • Primary Citation of Related Structures:  
    7WLY, 7WLZ

  • PubMed Abstract: 

    The SARS-CoV-2 Omicron variant harbors more than 30 mutations in the spike protein, leading to immune evasion from many therapeutic neutralizing antibodies. We reveal that a receptor-binding domain (RBD)-targeting monoclonal antibody, 35B5, exhibits potent neutralizing efficacy to Omicron. Cryo-electron microscopy structures of the extracellular domain trimer of Omicron spike with 35B5 Fab reveal that Omicron spike exhibits tight trimeric packing and high thermostability, as well as significant antigenic shifts and structural changes, within the RBD, N-terminal domain (NTD), and subdomains 1 and 2. However, these changes do not affect targeting of the invariant 35B5 epitope. 35B5 potently neutralizes SARS-CoV-2 Omicron and other variants by causing significant conformational changes within a conserved N-glycan switch that controls the transition of RBD from the "down" state to the "up" state, which allows recognition of the host entry receptor ACE2. This mode of action and potent neutralizing capacity of 35B5 indicate its potential therapeutic application for SARS-CoV-2.


  • Organizational Affiliation

    Department of Gastroenterology of the Second Affiliated Hospital, School of Medicine and Life Sciences Institute, Zhejiang University, Hangzhou 310058, China; MOE Laboratory for Biosystems Homeostasis and Protection, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B, C
1,285Severe acute respiratory syndrome coronavirus 2Mutation(s): 39 
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
Glycosylation
Glycosylation Sites: 9Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of 35B5 FabD [auth P]237Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Light chain of 35B5 FabE [auth O]219Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth C],
Y [auth C],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.98 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC3.3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China81530068
National Natural Science Foundation of China (NSFC)China81501717

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-25
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references
  • Version 1.2: 2022-06-22
    Changes: Database references