8G8C

Crystal structure of DH1322.1 Fab in complex with HIV proximal MPER peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Vaccine induction of heterologous HIV-1-neutralizing antibody B cell lineages in humans.

Williams, W.B.Alam, S.M.Ofek, G.Erdmann, N.Montefiori, D.C.Seaman, M.S.Wagh, K.Korber, B.Edwards, R.J.Mansouri, K.Eaton, A.Cain, D.W.Martin, M.Hwang, J.Arus-Altuz, A.Lu, X.Cai, F.Jamieson, N.Parks, R.Barr, M.Foulger, A.Anasti, K.Patel, P.Sammour, S.Parsons, R.J.Huang, X.Lindenberger, J.Fetics, S.Janowska, K.Niyongabo, A.Janus, B.M.Astavans, A.Fox, C.B.Mohanty, I.Evangelous, T.Chen, Y.Berry, M.Kirshner, H.Van Itallie, E.Saunders, K.O.Wiehe, K.Cohen, K.W.McElrath, M.J.Corey, L.Acharya, P.Walsh, S.R.Baden, L.R.Haynes, B.F.

(2024) Cell 187: 2919-2934.e20

  • DOI: https://doi.org/10.1016/j.cell.2024.04.033
  • Primary Citation of Related Structures:  
    8G8A, 8G8C, 8G8D

  • PubMed Abstract: 

    A critical roadblock to HIV vaccine development is the inability to induce B cell lineages of broadly neutralizing antibodies (bnAbs) in humans. In people living with HIV-1, bnAbs take years to develop. The HVTN 133 clinical trial studied a peptide/liposome immunogen targeting B cell lineages of HIV-1 envelope (Env) membrane-proximal external region (MPER) bnAbs (NCT03934541). Here, we report MPER peptide-liposome induction of polyclonal HIV-1 B cell lineages of mature bnAbs and their precursors, the most potent of which neutralized 15% of global tier 2 HIV-1 strains and 35% of clade B strains with lineage initiation after the second immunization. Neutralization was enhanced by vaccine selection of improbable mutations that increased antibody binding to gp41 and lipids. This study demonstrates proof of concept for rapid vaccine induction of human B cell lineages with heterologous neutralizing activity and selection of antibody improbable mutations and outlines a path for successful HIV-1 vaccine development.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DH1322.1 heavy chainA [auth H],
C [auth A]
233Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DH1322.1 light chainB [auth L],
D [auth B]
217Homo sapiensMutation(s): 0 
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Env polyproteinE [auth C],
F [auth P]
23Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P04578 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04578 
Go to UniProtKB:  P04578
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04578
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseG [auth D]3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.308α = 90
b = 182.95β = 92.28
c = 84.414γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Database references
  • Version 1.2: 2024-06-19
    Changes: Database references
  • Version 1.3: 2024-10-30
    Changes: Structure summary