5KG9

Crystal structure of the gp120 v2 antibody RE505-22 Fab from IGH- and IGK-humanized mouse

  • Classification: IMMUNE SYSTEM
  • Organism(s): Mus musculus, Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2016-06-13 Released: 2017-01-25 
  • Deposition Author(s): Nicely, N.I.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Immunodominance of Antibody Recognition of the HIV Envelope V2 Region in Ig-Humanized Mice.

Wiehe, K.Nicely, N.I.Lockwood, B.Kuraoka, M.Anasti, K.Arora, S.Bowman, C.M.Stolarchuk, C.Parks, R.Lloyd, K.E.Xia, S.M.Duffy, R.Shen, X.Kyratsous, C.A.Macdonald, L.E.Murphy, A.J.Scearce, R.M.Moody, M.A.Alam, S.M.Verkoczy, L.Tomaras, G.D.Kelsoe, G.Haynes, B.F.

(2017) J Immunol 198: 1047-1055

  • DOI: https://doi.org/10.4049/jimmunol.1601640
  • Primary Citation of Related Structures:  
    5KG9

  • PubMed Abstract: 

    In the RV144 gp120 HIV vaccine trial, decreased transmission risk was correlated with Abs that reacted with a linear epitope at a lysine residue at position 169 (K169) in the HIV-1 envelope (Env) V2 region. The K169 V2 response was restricted to Abs bearing Vλ rearrangements that expressed aspartic acid/glutamic acid in CDR L2. The AE.A244 gp120 in AIDSVAX B/E also bound to the unmutated ancestor of a V2-glycan broadly neutralizing Ab, but this Ab type was not induced in the RV144 trial. In this study, we sought to determine whether immunodominance of the V2 linear epitope could be overcome in the absence of human Vλ rearrangements. We immunized IgH- and Igκ-humanized mice with the AE.A244 gp120 Env. In these mice, the V2 Ab response was focused on a linear epitope that did not include K169. V2 Abs were isolated that used the same human VH gene segment as an RV144 V2 Ab but paired with a mouse λ L chain. Structural characterization of one of these V2 Abs revealed how the linear V2 epitope could be engaged, despite the lack of aspartic acid/glutamic acid encoded in the mouse repertoire. Thus, despite the absence of the human Vλ locus in these humanized mice, the dominance of Vλ pairing with human VH for HIV-1 Env V2 recognition resulted in human VH pairing with mouse λ L chains instead of allowing otherwise subdominant V2-glycan broadly neutralizing Abs to develop.


  • Organizational Affiliation

    Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710; kevin.wiehe@dm.duke.edu barton.haynes@dm.duke.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody RE505-22 Fab heavy chainA [auth H],
C [auth A]
221Mus musculusHomo sapiens
This entity is chimeric
Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antibody RE505-22 Fab light chainB [auth L],
D [auth B]
221Mus musculusHomo sapiens
This entity is chimeric
Mutation(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: 2.30 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.183α = 90
b = 76.749β = 90
c = 184.287γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2017-01-25 
  • Deposition Author(s): Nicely, N.I.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesUM1-AI100645

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-25
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.4: 2021-03-24
    Changes: Source and taxonomy
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description