8G8D

Crystal structure of DH1346 Fab in complex with HIV proximal MPER peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DH1346 heavy chainA [auth H],
D [auth A]
230Homo sapiensMutation(s): 0 
UniProt
Find proteins for P0DOX5 (Homo sapiens)
Explore P0DOX5 
Go to UniProtKB:  P0DOX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DOX5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DH1346 light chainB [auth L],
E [auth B]
215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
gp41 MPER peptideC [auth P],
F [auth C]
34Human 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
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth H]
H
I [auth H]
J [auth L]
K [auth L]
G [auth H],
H,
I [auth H],
J [auth L],
K [auth L],
L,
N [auth A],
O [auth A],
P [auth B],
Q [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
F
Query on F

Download Ideal Coordinates CCD File 
M [auth L]FLUORIDE ION
F
KRHYYFGTRYWZRS-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.02 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.069α = 90
b = 115.513β = 90
c = 231.322γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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