9BLX | pdb_00009blx

Rhesus macaque ITS111.01 Fab in complex with SIV MPER peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.178 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Isolation and structure of broad SIV-neutralizing antibodies reveal a proximal helical MPER epitope recognized by a rhesus multi-donor class.

Gorman, J.Du, R.Lai, Y.T.Ahmadi, M.S.King, H.A.D.Song, K.Manalang, K.Gonelli, C.A.Schramm, C.A.Cheng, C.Nguyen, R.Ambrozak, D.Druz, A.Shen, C.H.Yang, Y.Douek, D.C.Kwong, P.D.Roederer, M.Mason, R.D.

(2025) Cell Rep 44: 115163-115163

  • DOI: https://doi.org/10.1016/j.celrep.2024.115163
  • Primary Citation Related Structures: 
    9BLX, 9BNS, 9BP1

  • PubMed Abstract: 

    The membrane-proximal external region (MPER) of the HIV-1 envelope is a target for broadly neutralizing antibodies (bnAbs), and vaccine-elicited MPER-directed antibodies have recently been reported from a human clinical trial. In this study, we sought to identify MPER-directed nAbs in simian immunodeficiency virus (SIV)-infected rhesus macaques. We isolated four lineages of SIV MPER-directed nAbs from two SIV-infected macaques. The nAbs displayed low potency but up to 90% breadth on a 20-strain SIV panel. Crystal structures of representative nAbs in complex with SIV MPER peptides revealed the SIV antibodies to bind a helical epitope at the N-terminal (proximal) region of the MPER, defining a reproducible multi-donor class encompassing all four lineages. HIV-1 comparison showed that this class of SIV MPER-directed antibodies targets a helical region overlapping that targeted by human vaccine-elicited ones. Thus, a prevalent and reproducible class of SIV bnAbs recognizes an epitope similar to that recently observed in an HIV-1-vaccine trial.


  • Organizational Affiliation
    • Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA; Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA. Electronic address: jason.gorman@fda.hhs.gov.

Macromolecule Content 

  • Total Structure Weight: 103.32 kDa 
  • Atom Count: 7,409 
  • Modeled Residue Count: 903 
  • Deposited Residue Count: 944 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ITS111.01 HeavyA [auth H],
C [auth A]
232Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ITS111.01 LightB [auth L],
D [auth B]
213Macaca mulattaMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Envelope glycoprotein gp160E [auth I],
F [auth G]
27Simian immunodeficiency virusMutation(s): 0 
UniProt
Find proteins for A0A4Y5TJX4 (Simian immunodeficiency virus)
Explore A0A4Y5TJX4 
Go to UniProtKB:  A0A4Y5TJX4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A4Y5TJX4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.178 (Depositor), 0.178 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.865α = 90
b = 118.834β = 104.705
c = 66.541γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
HKL-2000data reduction
PHENIXphasing

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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-15
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Database references