6VOR

Crystal structure of macaque anti-HIV-1 antibody RM20E1

  • Classification: IMMUNE SYSTEM
  • Organism(s): Macaca mulatta
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2020-01-31 Released: 2020-09-16 
  • Deposition Author(s): Yuan, M., Wilson, I.A.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report

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This is version 1.1 of the entry. See complete history


Literature

Mapping the immunogenic landscape of near-native HIV-1 envelope trimers in non-human primates.

Cottrell, C.A.van Schooten, J.Bowman, C.A.Yuan, M.Oyen, D.Shin, M.Morpurgo, R.van der Woude, P.van Breemen, M.Torres, J.L.Patel, R.Gross, J.Sewall, L.M.Copps, J.Ozorowski, G.Nogal, B.Sok, D.Rakasz, E.G.Labranche, C.Vigdorovich, V.Christley, S.Carnathan, D.G.Sather, D.N.Montefiori, D.Silvestri, G.Burton, D.R.Moore, J.P.Wilson, I.A.Sanders, R.W.Ward, A.B.van Gils, M.J.

(2020) PLoS Pathog 16: e1008753-e1008753

  • DOI: https://doi.org/10.1371/journal.ppat.1008753
  • Primary Citation of Related Structures:  
    6VOR, 6VOS, 6VSR

  • PubMed Abstract: 

    The induction of broad and potent immunity by vaccines is the key focus of research efforts aimed at protecting against HIV-1 infection. Soluble native-like HIV-1 envelope glycoproteins have shown promise as vaccine candidates as they can induce potent autologous neutralizing responses in rabbits and non-human primates. In this study, monoclonal antibodies were isolated and characterized from rhesus macaques immunized with the BG505 SOSIP.664 trimer to better understand vaccine-induced antibody responses. Our studies reveal a diverse landscape of antibodies recognizing immunodominant strain-specific epitopes and non-neutralizing neo-epitopes. Additionally, we isolated a subset of mAbs against an epitope cluster at the gp120-gp41 interface that recognize the highly conserved fusion peptide and the glycan at position 88 and have characteristics akin to several human-derived broadly neutralizing antibodies.


  • Organizational Affiliation

    Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California, United States of America.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
RM20E1 Fab heavy chain
A, C
227Macaca mulattaMutation(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
RM20E1 Fab light chain
B, D
219Macaca mulattaMutation(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: 1.85 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.369α = 98.74
b = 57.741β = 94.05
c = 92.745γ = 97.83
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
xia2data reduction
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 StatesUM1 AI100663
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01 AI110657

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description