4B50 | pdb_00004b50

Crystal structure of the HIV-1 gp41 MPER-specific llama VHH 2H10

• PDB DOI: https://doi.org/10.2210/pdb4B50/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Lama glama
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-08-02 Released: 2013-03-27 
• Deposition Author(s): Lutje Hulsik, D., Sabin, C., Macheboeuf, P., Weissenhorn, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.180 (Depositor), 0.177 (DCC) 
• R-Value Work: 
  0.145 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.147 (Depositor) 

Starting Model: experimental

Literature

A Gp41 Mper-Specific Llama Vhh Requires a Hydrophobic Cdr3 for Neutralization But not for Antigen Recognition.

Lutje Hulsik, D., Liu, Y.Y., Strokappe, N.M., Battella, S., El Khattabi, M., Mccoy, L.E., Sabin, C., Hinz, A., Hock, M., Macheboeuf, P., Bonvin, A.M., Langedijk, J.P., Davis, D., Forsman Quigley, A., Aasa-Chapman, M.M., Seaman, M.S., Ramos, A., Poignard, P., Favier, A., Simorre, J.P., Weiss, R.A., Verrips, C.T., Weissenhorn, W., Rutten, L.

(2013) PLoS Pathog 9: 3202

• PubMed: 23505368 
• DOI: https://doi.org/10.1371/journal.ppat.1003202
• Primary Citation Related Structures: 
  4B50


• PubMed Abstract: 
  

  The membrane proximal external region (MPER) of the HIV-1 glycoprotein gp41 is targeted by the broadly neutralizing antibodies 2F5 and 4E10. To date, no immunization regimen in animals or humans has produced HIV-1 neutralizing MPER-specific antibodies. We immunized llamas with gp41-MPER proteoliposomes and selected a MPER-specific single chain antibody (VHH), 2H10, whose epitope overlaps with that of mAb 2F5. Bi-2H10, a bivalent form of 2H10, which displayed an approximately 20-fold increased affinity compared to the monovalent 2H10, neutralized various sensitive and resistant HIV-1 strains, as well as SHIV strains in TZM-bl cells. X-ray and NMR analyses combined with mutagenesis and modeling revealed that 2H10 recognizes its gp41 epitope in a helical conformation. Notably, tryptophan 100 at the tip of the long CDR3 is not required for gp41 interaction but essential for neutralization. Thus bi-2H10 is an anti-MPER antibody generated by immunization that requires hydrophobic CDR3 determinants in addition to epitope recognition for neutralization similar to the mode of neutralization employed by mAbs 2F5 and 4E10.

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Organizational Affiliation: 
• Unit of Virus Host Cell Interactions (UVHCI), UMI 3265, Université Joseph Fourier-EMBL-CNRS, Grenoble, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 13.35 kDa 
• Atom Count: 1,235 
• Modeled Residue Count: 122 
• Deposited Residue Count: 122 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
2H10 LLAMA VHH	A	122	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free:  0.180 (Depositor), 0.177 (DCC) 
• R-Value Work:  0.145 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.147 (Depositor) 

Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.95	α = 90
b = 89.95	β = 90
c = 89.95	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-27 
Deposition Author(s): Lutje Hulsik, D., Sabin, C., Macheboeuf, P., Weissenhorn, W.

Revision History  

• Version 1.0: 2013-03-27
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary