7L6M

Cryo-EM structure of DH898.1 Fab-dimer from local refinement of the Fab-dimer bound near the CD4 binding site of HIV-1 Env CH848 SOSIP trimer


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.3 of the entry. See complete history


Literature

Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.

Williams, W.B.Meyerhoff, R.R.Edwards, R.J.Li, H.Manne, K.Nicely, N.I.Henderson, R.Zhou, Y.Janowska, K.Mansouri, K.Gobeil, S.Evangelous, T.Hora, B.Berry, M.Abuahmad, A.Y.Sprenz, J.Deyton, M.Stalls, V.Kopp, M.Hsu, A.L.Borgnia, M.J.Stewart-Jones, G.B.E.Lee, M.S.Bronkema, N.Moody, M.A.Wiehe, K.Bradley, T.Alam, S.M.Parks, R.J.Foulger, A.Oguin, T.Sempowski, G.D.Bonsignori, M.LaBranche, C.C.Montefiori, D.C.Seaman, M.Santra, S.Perfect, J.Francica, J.R.Lynn, G.M.Aussedat, B.Walkowicz, W.E.Laga, R.Kelsoe, G.Saunders, K.O.Fera, D.Kwong, P.D.Seder, R.A.Bartesaghi, A.Shaw, G.M.Acharya, P.Haynes, B.F.

(2021) Cell 184: 2955

  • DOI: https://doi.org/10.1016/j.cell.2021.04.042
  • Primary Citation of Related Structures:  
    6VTU, 6XRJ, 7L02, 7L06, 7L09, 7L6M, 7L6O, 7LU9, 7LUA

  • PubMed Abstract: 

    Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (V H ) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without V H -swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgM + IgD + CD27 + , thus suggesting that they originated from a pool of antigen-experienced IgM + or marginal zone B cells.


  • Organizational Affiliation

    Duke Human Vaccine Institute, Durham, NC 27710, USA; Department of Medicine, Duke University, Durham, NC 27710, USA. Electronic address: wilton.williams@duke.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DH898.1 Fab light chainA [auth g],
D [auth j]
218Macaca mulattaMutation(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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DH898.1 Fab heavy chainB [auth h],
C [auth i]
219Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX
MODEL REFINEMENTISOLDE

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 StatesAI145687

Revision History  (Full details and data files)

  • Version 1.0: 2021-02-10
    Type: Initial release
  • Version 2.0: 2021-03-24
    Type: Coordinate replacement
    Reason: Sequence discrepancy
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary
  • Version 2.1: 2021-06-02
    Changes: Database references
  • Version 2.2: 2021-06-09
    Changes: Database references
  • Version 2.3: 2024-11-13
    Changes: Data collection, Database references, Structure summary