6XRJ

Crystal structure of the disulfide linked DH717.1 Fab dimer, derived from a macaque HIV-1 vaccine-induced Env glycan-reactive neutralizing antibody B cell lineage


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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
DH717.1 heavy chain Fab fragmentA,
C,
E,
G [auth H]
226Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DH717.1 light chain Fab fragmentB,
D,
F,
H [auth L]
211Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.246 
  • Space Group: P 43 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 201.587α = 90
b = 201.587β = 90
c = 154.327γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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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: 2020-12-30
    Type: Initial release
  • Version 1.1: 2021-06-02
    Changes: Database references
  • Version 1.2: 2021-06-09
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary