7RYV | pdb_00007ryv

Anti-HIV neutralizing antibody Ab1573 Fab isolated from sequentially immunized macaques

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

  • Deposited: 2021-08-26 Released: 2022-01-19 
  • Deposition Author(s): Yang, Z., Bjorkman, P.J.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Bill & Melinda Gates Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.254 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7RYV

This is version 1.4 of the entry. See complete history

Literature

Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer.

Yang, Z.Dam, K.A.Bridges, M.D.Hoffmann, M.A.G.DeLaitsch, A.T.Gristick, H.B.Escolano, A.Gautam, R.Martin, M.A.Nussenzweig, M.C.Hubbell, W.L.Bjorkman, P.J.

(2022) Nat Commun 13: 732-732

  • DOI: https://doi.org/10.1038/s41467-022-28424-3
  • Primary Citation Related Structures: 
    7RYU, 7RYV, 7TFN, 7TFO

  • PubMed Abstract: 

    Broadly-neutralizing antibodies (bNAbs) against HIV-1 Env can protect from infection. We characterize Ab1303 and Ab1573, heterologously-neutralizing CD4-binding site (CD4bs) antibodies, isolated from sequentially-immunized macaques. Ab1303/Ab1573 binding is observed only when Env trimers are not constrained in the closed, prefusion conformation. Fab-Env cryo-EM structures show that both antibodies recognize the CD4bs on Env trimer with an 'occluded-open' conformation between closed, as targeted by bNAbs, and fully-open, as recognized by CD4. The occluded-open Env trimer conformation includes outwardly-rotated gp120 subunits, but unlike CD4-bound Envs, does not exhibit V1V2 displacement, 4-stranded gp120 bridging sheet, or co-receptor binding site exposure. Inter-protomer distances within trimers measured by double electron-electron resonance spectroscopy suggest an equilibrium between occluded-open and closed Env conformations, consistent with Ab1303/Ab1573 binding stabilizing an existing conformation. Studies of Ab1303/Ab1573 demonstrate that CD4bs neutralizing antibodies that bind open Env trimers can be raised by immunization, thereby informing immunogen design and antibody therapeutic efforts.


  • Organizational Affiliation
    • Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.

Macromolecule Content 

  • Total Structure Weight: 189.07 kDa 
  • Atom Count: 13,616 
  • Modeled Residue Count: 1,725 
  • Deposited Residue Count: 1,776 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ab1573 Fab heavy chainA [auth E],
C [auth H],
D [auth I],
G [auth P]
228Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ab1573 Fab light chainB [auth F],
E [auth J],
F [auth L],
H [auth Q]
216Macaca mulattaMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.254 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.224 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.502α = 90
b = 138.396β = 95.71
c = 83.727γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
TRUNCATEdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesHIVRAD P01 AI100148
Bill & Melinda Gates FoundationUnited StatesCAVD INV-002143

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-19
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2022-02-23
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary