7TB4

Cryo-EM structure of the spike of SARS-CoV-2 Omicron variant of concern


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Antibodies with potent and broad neutralizing activity against antigenically diverse and highly transmissible SARS-CoV-2 variants.

Wang, L.Zhou, T.Zhang, Y.Yang, E.S.Schramm, C.A.Shi, W.Pegu, A.Oloninyi, O.K.Ransier, A.Darko, S.Narpala, S.R.Hatcher, C.Martinez, D.R.Tsybovsky, Y.Phung, E.Abiona, O.M.Cale, E.M.Chang, L.A.Corbett, K.S.DiPiazza, A.T.Gordon, I.J.Leung, K.Liu, T.Mason, R.D.Nazzari, A.Novik, L.Olia, A.S.Doria-Rose, N.A.Stephens, T.Stringham, C.D.Talana, C.A.Teng, I.T.Wagner, D.Widge, A.T.Zhang, B.Roederer, M.Ledgerwood, J.E.Ruckwardt, T.J.Gaudinski, M.R.Baric, R.S.Graham, B.S.McDermott, A.B.Douek, D.C.Kwong, P.D.Mascola, J.R.Sullivan, N.J.Misasi, J.

(2021) Biorxiv 

  • DOI: 10.1101/2021.02.25.432969
  • Primary Citation of Related Structures:  
    7TB4

  • PubMed Abstract: 
  • The emergence of highly transmissible SARS-CoV-2 variants of concern (VOC) that are resistant to therapeutic antibodies highlights the need for continuing discovery of broadly reactive antibodies. We identify four receptor-binding domain targeting antibodies from three early-outbreak convalescent donors with potent neutralizing activity against 12 variants including the B ...

    The emergence of highly transmissible SARS-CoV-2 variants of concern (VOC) that are resistant to therapeutic antibodies highlights the need for continuing discovery of broadly reactive antibodies. We identify four receptor-binding domain targeting antibodies from three early-outbreak convalescent donors with potent neutralizing activity against 12 variants including the B.1.1.7 and B.1.351 VOCs. Two of them are ultrapotent, with sub-nanomolar neutralization titers (IC50 <0.0006 to 0.0102 μ g/mL; IC80 < 0.0006 to 0.0251 μ g/mL). We define the structural and functional determinants of binding for all four VOC-targeting antibodies, and show that combinations of two antibodies decrease the in vitro generation of escape mutants, suggesting potential means to mitigate resistance development. These results define the basis of therapeutic cocktails against VOCs and suggest that targeted boosting of existing immunity may increase vaccine breadth against VOCs.


    Organizational Affiliation

    Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Surface glycoproteinA, B, C1192Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: S
UniProt
Find proteins for A0A8A4XEV3 (Severe acute respiratory syndrome coronavirus 2)
Explore A0A8A4XEV3 
Go to UniProtKB:  A0A8A4XEV3
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D, E, F, G, H, I, J, K
D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R
2N/AN-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth A] , BA [auth A] , CA [auth A] , DA [auth B] , EA [auth B] , FA [auth B] , GA [auth B] , HA [auth B] , 
AA [auth A], BA [auth A], CA [auth A], DA [auth B], EA [auth B], FA [auth B], GA [auth B], HA [auth B], IA [auth B], JA [auth B], KA [auth B], LA [auth B], MA [auth B], NA [auth C], OA [auth C], PA [auth C], QA [auth C], RA [auth C], S [auth A], SA [auth C], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]
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: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesIntramural

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-01-19
    Changes: Database references