7M71

SARS-CoV-2 Spike:5A6 Fab complex I focused refinement


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7kqb


Literature

Structural insight into SARS-CoV-2 neutralizing antibodies and modulation of syncytia.

Asarnow, D.Wang, B.Lee, W.H.Hu, Y.Huang, C.W.Faust, B.Ng, P.M.L.Ngoh, E.Z.X.Bohn, M.Bulkley, D.Pizzorno, A.Ary, B.Tan, H.C.Lee, C.Y.Minhat, R.A.Terrier, O.Soh, M.K.Teo, F.J.Yeap, Y.Y.C.Seah, S.G.K.Chan, C.E.Z.Connelly, E.Young, N.J.Maurer-Stroh, S.Renia, L.Hanson, B.J.Rosa-Calatrava, M.Manglik, A.Cheng, Y.Craik, C.S.Wang, C.I.

(2021) Cell 184: 3192

  • DOI: https://doi.org/10.1016/j.cell.2021.04.033
  • Primary Citation of Related Structures:  
    7KQB, 7KQE, 7M71, 7M7B

  • PubMed Abstract: 

    Infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is initiated by binding of the viral Spike protein to host receptor angiotensin-converting enzyme 2 (ACE2), followed by fusion of viral and host membranes. Although antibodies that block this interaction are in emergency use as early coronavirus disease 2019 (COVID-19) therapies, the precise determinants of neutralization potency remain unknown. We discovered a series of antibodies that potently block ACE2 binding but exhibit divergent neutralization efficacy against the live virus. Strikingly, these neutralizing antibodies can inhibit or enhance Spike-mediated membrane fusion and formation of syncytia, which are associated with chronic tissue damage in individuals with COVID-19. As revealed by cryoelectron microscopy, multiple structures of Spike-antibody complexes have distinct binding modes that not only block ACE2 binding but also alter the Spike protein conformational cycle triggered by ACE2 binding. We show that stabilization of different Spike conformations leads to modulation of Spike-mediated membrane fusion with profound implications for COVID-19 pathology and immunity.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco (UCSF) School of Medicine, San Francisco, CA, USA; QBI COVID-19 Research Group (QCRG), San Francisco, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Spike glycoprotein
A, B
1,208Severe acute respiratory syndrome coronavirus 2Mutation(s): 5 
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: 2Go to GlyGen: P0DTC2-1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 5A6 Fab heavy chainC [auth H]449Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody 5A6 Fab light chainD [auth L]214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.66 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.15.0
RECONSTRUCTIONcryoSPARC3.1.0
MODEL REFINEMENTISOLDE1.0
MODEL REFINEMENTCoot0.9.4.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP50AI150476
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD020054
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesS10OD021741

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Refinement description, Structure summary