7JWB

SARS CoV2 Spike ectodomain with engineered trimerized VH binder


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Bi-paratopic and multivalent VH domains block ACE2 binding and neutralize SARS-CoV-2.

Bracken, C.J.Lim, S.A.Solomon, P.Rettko, N.J.Nguyen, D.P.Zha, B.S.Schaefer, K.Byrnes, J.R.Zhou, J.Lui, I.Liu, J.Pance, K.Zhou, X.X.Leung, K.K.Wells, J.A.

(2021) Nat Chem Biol 17: 113-121

  • DOI: 10.1038/s41589-020-00679-1
  • Primary Citation of Related Structures:  
    7JWB

  • PubMed Abstract: 
  • Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angiotensin-converting enzyme 2 (ACE2) binding interface of the SARS-CoV-2 Spike receptor-binding domain (Spike-RBD) ...

    Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angiotensin-converting enzyme 2 (ACE2) binding interface of the SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified VH binders to two non-overlapping epitopes and further assembled these into multivalent and bi-paratopic formats. These VH constructs showed increased affinity to Spike (up to 600-fold) and neutralization potency (up to 1,400-fold) on pseudotyped SARS-CoV-2 virus when compared to standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with a half-maximal inhibitory concentration (IC 50 ) of 4.0 nM (180 ng ml -1 ). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain engaging an RBD at the ACE2 binding site, confirming our original design strategy.


    Related Citations: 
    • Bi-paratopic and multivalent human VH domains neutralize SARS-CoV-2 by targeting distinct epitopes within the ACE2 binding interface of Spike.
      Bracken, C.J., Lim, S.A., Solomon, P., Rettko, N.J., Nguyen, D.P., Zha, B.S., Schaefer, K., Byrnes, J.R., Zhou, J., Lui, I., Liu, J., Pance, K., Zhou, X.X., Leung, K.K., Wells, J.A.
      (2020) Biorxiv --: --

    Organizational Affiliation

    Chan Zuckerberg Biohub, San Francisco, CA, USA. jim.wells@ucsf.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
autonomous human heavy chain variable domainA [auth D]421Homo sapiensMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Spike glycoproteinB [auth A],
C [auth B],
D [auth C]
1208Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.00 Å
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Defense Advanced Research Projects Agency (DARPA)United StatesHR0011-19-2-0020
Quantitative Biosciences InstituteUnited States--
FastGrantsUnited States--
Laboratory for Genomics Research (LGR)United StatesExcellence in Research Award (ERA)

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2020-10-14
    Changes: Database references
  • Version 1.2: 2020-12-16
    Changes: Database references
  • Version 1.3: 2020-12-30
    Changes: Database references