7N08

Crystal structure of the 3D6 antibody fragment bound to the HIV-1 gp41 immunodominant region

  • Classification: IMMUNE SYSTEM
  • Organism(s): HIV-1 06TG.HT008, Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2021-05-25 Released: 2022-03-30 
  • Deposition Author(s): Cook, J.D., Lee, J.E.
  • Funding Organization(s): Canadian Institutes of Health Research (CIHR), Ontario Early Researcher Awards, Canada Research Chairs, Canada Foundation for Innovation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Conformational plasticity of the HIV-1 gp41 immunodominant region is recognized by multiple non-neutralizing antibodies.

Cook, J.D., Khondker, A., Lee, J.E.

(2022) Commun Biol 5: 291-291

  • DOI: 10.1038/s42003-022-03235-w
  • Primary Citation of Related Structures:  
    7N04, 7N05, 7N07, 7N08

  • PubMed Abstract: 

    • The early humoral immune response to acute HIV-1 infection is largely non-neutralizing. The principal target of these antibodies is the primary immunodominant region (PID) on the gp41 fusion protein. The PID is a highly conserved 15-residue region displayed on the surface of HIV-1 virions ...

    The early humoral immune response to acute HIV-1 infection is largely non-neutralizing. The principal target of these antibodies is the primary immunodominant region (PID) on the gp41 fusion protein. The PID is a highly conserved 15-residue region displayed on the surface of HIV-1 virions. In this study, we analyzed the humoral determinants of HIV-1 gp41 PID binding using biophysical, structural, and computational methods. In complex with a patient-derived near-germline antibody fragment, the PID motif adopts an elongated random coil, whereas the PID bound to affinity-matured Fab adopts a strand-turn-helix conformation. Molecular dynamics simulations showed that the PID is structurally plastic suggesting that the PID can form an ensemble of structural states recognized by various non-neutralizing antibodies, facilitating HIV-1 immunodominance observed in acute and chronic HIV-1 infections. An improved understanding of how the HIV-1 gp41 PID misdirects the early humoral response should guide the development of an effective HIV-1 vaccine.

    Organizational Affiliation: 

    Department of Laboratory Medicine and Pathobiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, M5S 1A8, Canada. jeff.lee@utoronto.ca.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HIV-1 gp41 immunodominant regionD [auth E],
C [auth F],
A [auth G]		15HIV-1 06TG.HT008Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab 3D6 heavy chainG [auth A],
I [auth C],
B [auth H]		247Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fab 3D6 light chainF [auth B],
H [auth D],
E [auth L]		212Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.825α = 90
b = 77.825β = 90
c = 218.972γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2021-05-25 
  • Released Date: 2022-03-30 
    • Deposition Author(s): Cook, J.D., Lee, J.E.
Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-115066
Canadian Institutes of Health Research (CIHR)CanadaPJT-173301
Ontario Early Researcher AwardsCanadaER-13-09-116
Canada Research ChairsCanada950-231672
Canada Foundation for InnovationCanada--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Database references