6XOC | pdb_00006xoc

Crystal structure of glVRC01 Fab in complex with anti-idiotypic iv4 Fab

• PDB DOI: https://doi.org/10.2210/pdb6XOC/pdb

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


• Deposited: 2020-07-06 Released: 2021-03-31 
• Deposition Author(s): Aljedani, S.S., Weidle, C., Pancera, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free: 
  0.240 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 
  0.201 (Depositor) 

Starting Model: experimental

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

• PubMed: 33951425 
• 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.

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Organizational Affiliation: 
• Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA.
Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98195, USA; University of Washington, Department of Immunology, Seattle, WA 98109, USA.
Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98195, USA. Electronic address: [e-mail].
Fred Hutchinson Cancer Research Center, Vaccines and Infectious Diseases Division, Seattle, WA 98109, USA; University of Washington, Department of Global Health, Seattle, WA 98195, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 4-mer - A4 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 95.63 kDa 
• Atom Count: 6,818 
• Modeled Residue Count: 859 
• Deposited Residue Count: 866 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iv4 Fab Heavy Chain	A	221	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IV4 Fab Light Chain	B	217	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
iGL-VRC01 Fab Heavy Chain	C [auth H]	221	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
iGL-VRC01 Fab Light Chain	D [auth L]	207	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	O [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	M [auth A], Q [auth B], U [auth L]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], P [auth B], R [auth H], S [auth L], T [auth L]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
SCN	N [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M
K	E [auth A], F [auth A], G [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.45 Å
• R-Value Free:  0.240 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.203 (DCC) 
• R-Value Observed: 0.201 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.016	α = 90
b = 114.417	β = 90
c = 220.969	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
Coot	model building
PHASER	phasing
HKL-2000	data reduction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Aljedani, S.S., Weidle, C., Pancera, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• 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: 2024-11-06
  Changes: Structure summary