7JLK

Crystal structure of glVRC01 Fab in complex with anti-idiotype iv1 scFv


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 1.2 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 of 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
iv1 Heavy ChainA [auth H]133Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
glVRC01 Heavy ChainB [auth A]233Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
glVRC01 Light ChainC [auth B]210Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
iv1 Light ChainD [auth L]122Mus musculusMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
EA [auth B],
FA [auth B],
GA [auth B],
HA [auth B],
P [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
IA [auth B],
JA [auth B],
Q [auth A],
RA [auth L]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
G [auth H]
AA [auth B],
BA [auth B],
CA [auth B],
DA [auth B],
G [auth H],
H,
I [auth H],
N [auth A],
NA [auth L],
O [auth A],
OA [auth L],
PA [auth L],
QA [auth L],
Z [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth H]
F [auth H]
J [auth A]
K [auth A]
KA [auth L]
E [auth H],
F [auth H],
J [auth A],
K [auth A],
KA [auth L],
L [auth A],
LA [auth L],
M [auth A],
MA [auth L],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
W [auth B],
X [auth B],
Y [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.182 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.019α = 90
b = 85.244β = 99.733
c = 113.636γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
Cootmodel building
Blu-Icedata collection
HKL-2000data scaling

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 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