8VS8 | pdb_00008vs8

Crystal structure of ADI-19425 Fab in complex with anti-idiotypic 1D3 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free: 
    0.273 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8VS8

This is version 1.2 of the entry. See complete history

Literature

Targeting RSV-neutralizing B cell receptors with anti-idiotypic antibodies.

Scharffenberger, S.C.Wan, Y.H.Homad, L.J.Kher, G.Haynes, A.M.Poudel, B.Sinha, I.R.Aldridge, N.Pai, A.Bibby, M.Chhan, C.B.Davis, A.R.Moodie, Z.Palacio, M.B.Escolano, A.McElrath, M.J.Boonyaratanakornkit, J.Pancera, M.McGuire, A.T.

(2024) Cell Rep 43: 114811-114811

  • DOI: https://doi.org/10.1016/j.celrep.2024.114811
  • Primary Citation Related Structures: 
    8VS7, 8VS8

  • PubMed Abstract: 

    Respiratory syncytial virus (RSV) causes lower respiratory tract infections with significant morbidity and mortality at the extremes of age. Vaccines based on the viral fusion protein are approved for adults over 60, but infant protection relies on passive immunity via antibody transfer or maternal vaccination. An infant vaccine that rapidly elicits protective antibodies would fulfill a critical unmet need. Antibodies arising from the VH3-21/VL1-40 gene pairing can neutralize RSV without the need for affinity maturation, making them attractive to target through vaccination. Here, we develop an anti-idiotypic monoclonal antibody (ai-mAb) immunogen that is specific for unmutated VH3-21/VL1-40 B cell receptors (BCRs). The ai-mAb efficiently engages B cells with bona fide target BCRs and does not activate off-target non-neutralizing B cells, unlike recombinant pre-fusion (preF) protein used in current RSV vaccines. These results establish proof of concept for using an ai-mAb-derived vaccine to target B cells hardwired to produce RSV-neutralizing antibodies.


  • Organizational Affiliation
    • Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA; Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA.

Macromolecule Content 

  • Total Structure Weight: 757.47 kDa 
  • Atom Count: 45,030 
  • Modeled Residue Count: 5,948 
  • Deposited Residue Count: 7,080 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ADI-19425 Heavy Chain
A,
CA [auth c],
E,
I,
M,
Q,
U,
Y
227Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
ADI-19425 Light Chain
B,
DA [auth d],
F,
J,
N,
R,
V,
Z
218Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
1D3 Light Chain214Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
1D3 Heavy Chain226Homo sapiensMutation(s): 0 

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PCA
Query on PCA
B
DA [auth d]
F
J
N
B,
DA [auth d],
F,
J,
N,
R,
V,
Z
L-PEPTIDE LINKINGC5 H7 N O3GLN

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.67 Å
  • R-Value Free:  0.273 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.233 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.069α = 83.98
b = 149.981β = 89.9
c = 164.43γ = 74.61
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

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 StatesR21AI156063

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-18
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2026-04-01
    Changes: Database references