6AVN

Crystal structure of unbound anti-HIV antibody Fab PGV19 at 2.5 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of a cleavage-independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer.

Sarkar, A.Bale, S.Behrens, A.J.Kumar, S.Sharma, S.K.de Val, N.Pallesen, J.Irimia, A.Diwanji, D.C.Stanfield, R.L.Ward, A.B.Crispin, M.Wyatt, R.T.Wilson, I.A.

(2018) Nat Commun 9: 1956-1956

  • DOI: https://doi.org/10.1038/s41467-018-04272-y
  • Primary Citation of Related Structures:  
    6AVN, 6B0N

  • PubMed Abstract: 

    Furin cleavage of the HIV envelope glycoprotein is an essential step for cell entry that enables formation of well-folded, native-like glycosylated trimers, releases constraints on the fusion peptide, and limits enzymatic processing of the N-glycan shield. Here, we show that a cleavage-independent, stabilized, soluble Env trimer mimic (BG505 NFL.664) exhibits a "closed-form", native-like, prefusion conformation akin to furin-cleaved Env trimers. The crystal structure of BG505 NFL.664 at 3.39 Å resolution with two potent bNAbs also identifies the full epitopes of PGV19 and PGT122 that target the receptor binding site and N332 supersite, respectively. Quantitative site-specific analysis of the glycan shield reveals that native-like glycan processing is maintained despite furin-independent maturation in the secretory pathway. Thus, cleavage-independent NFL Env trimers exhibit quaternary protein and carbohydrate structures similar to the native viral spike that further validate their potential as vaccine immunogen candidates.


  • Organizational Affiliation

    IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, 92037, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PGV19 Fab heavy chainA [auth H]223Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PGV19 Fab light chainB [auth L]209Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.783α = 90
b = 69.783β = 90
c = 193.28γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary