6MNS

Rhesus macaque anti-HIV V3 antibody DH753 with gp120 V3 ZAM18 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Difficult-to-neutralize global HIV-1 isolates are neutralized by antibodies targeting open envelope conformations.

Han, Q.Jones, J.A.Nicely, N.I.Reed, R.K.Shen, X.Mansouri, K.Louder, M.Trama, A.M.Alam, S.M.Edwards, R.J.Bonsignori, M.Tomaras, G.D.Korber, B.Montefiori, D.C.Mascola, J.R.Seaman, M.S.Haynes, B.F.Saunders, K.O.

(2019) Nat Commun 10: 2898-2898

  • DOI: https://doi.org/10.1038/s41467-019-10899-2
  • Primary Citation of Related Structures:  
    6MNQ, 6MNR, 6MNS

  • PubMed Abstract: 

    The HIV-1 envelope (Env) is the target for neutralizing antibodies and exists on the surface of virions in open or closed conformations. Difficult-to-neutralize viruses (tier 2) express Env in a closed conformation antigenic for broadly neutralizing antibodies (bnAbs) but not for third variable region (V3) antibodies. Here we show that select V3 macaque antibodies elicited by Env vaccination can neutralize 26% of otherwise tier 2 HIV-1 isolates in standardized virus panels. The V3 antibodies only bound to Env in its open conformation. Thus, Envs on tier 2 viruses sample a state where the V3 loop is not in its closed conformation position. Envelope second variable region length, glycosylation sites and V3 amino acids were signatures of neutralization sensitivity. This study determined that open conformations of Env with V3 exposed are present on a subset of otherwise neutralization-resistant virions, therefore neutralization of tier 2 HIV-1 does not always indicate bnAb induction.


  • Organizational Affiliation

    Department of Medicine, Duke University Medical Center, Durham, NC, 27710, USA.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Envelope glylcoproteinA [auth P],
D [auth Q]
23Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P05877 (Human immunodeficiency virus type 1 group M subtype B (isolate MN))
Explore P05877 
Go to UniProtKB:  P05877
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05877
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ab DH753 heavy chain Fab fragmentB [auth H],
E [auth A]
227Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ab DH753 light chainC [auth L],
F [auth B]
216Macaca mulattaMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.92α = 90
b = 138.315β = 91.55
c = 71.678γ = 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: 2019-07-24 
  • Deposition Author(s): Nicely, N.I.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-AI120801
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: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.2: 2024-04-03
    Changes: Data collection, Database references, Refinement description