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 7JLN | pdb_00007jln

Crystal structure of glVRC01 Fab in complex with anti-idiotype iv9 Fab


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 
    0.256 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7JLN

This is version 1.3 of the entry. See complete history. 

Literature

Development of a VRC01-class germline targeting immunogen derived from anti-idiotypic antibodies.

Seydoux, E., Wan, Y.H., Feng, J., Wall, A., Aljedani, S., Homad, L.J., MacCamy, A.J., Weidle, C., Gray, M.D., Brumage, L., Taylor, J.J., Pancera, M., Stamatatos, L., McGuire, A.T.

(2021) Cell Rep 35: 109084-109084

  • DOI: https://doi.org/10.1016/j.celrep.2021.109084
  • Primary Citation Related Structures: 
    6VRQ, 6XOC, 7JLK, 7JLN

  • PubMed Abstract: 

    An effective HIV-1 vaccine will likely need to elicit broadly neutralizing antibodies (bNAbs). Broad and potent VRC01-class bNAbs have been isolated from multiple infected individuals, suggesting that they could be reproducibly elicited by vaccination. Several HIV-1 envelope-derived germline-targeting immunogens have been designed to engage naive VRC01-class precursor B cells. However, they also present off-target epitopes that could hinder development of VRC01-class bNAbs. We characterize a panel of anti-idiotypic monoclonal antibodies (ai-mAbs) raised against inferred-germline (iGL) VRC01-class antibodies. By leveraging binding, structural, and B cell sorting data, we engineered a bispecific molecule derived from two ai-mAbs; one specific for VRC01-class heavy chains and one specific for VRC01-class light chains. The bispecific molecule preferentially activates iGL-VRC01 B cells in vitro and induces specific antibody responses in a murine adoptive transfer model with a diverse polyclonal B cell repertoire. This molecule represents an alternative non-envelope-derived germline-targeting immunogen that can selectively activate VRC01-class precursors in vivo.


  • Organizational Affiliation: 
    • Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA.

Macromolecule Content 

  • Total Structure Weight: 96.63 kDa 
  • Atom Count: 6,791 
  • Modeled Residue Count: 857 
  • Deposited Residue Count: 888 
  • Unique protein chains: 4

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
iv9 Heavy Chain225Mus musculusMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
iv9 Light Chain220Mus musculusMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
glVRC01 Heavy ChainC [auth H]233Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
glVRC01 Light ChainD [auth L]210Homo sapiensMutation(s): 0 
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains Modified ResidueModification TypeFormula2D Diagram
PCA
Query on PCA
GLNPyrrolidone carboxylic acidC5 H7 N O3

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free:  0.256 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.199 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.42α = 90
b = 50.073β = 93.103
c = 125.171γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
HKL-2000data reduction
SCALEPACKdata scaling
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 States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-31
    Type: Initial release
  • Version 1.1: 2021-05-19
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary