5KJR

Crystal structure of the ADCC-potent antibody N60-i3 Fab in complex with HIV-1 Clade A/E gp120 W69A/S115W mutant and M48U1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 

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Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history


Literature

A Highly Conserved gp120 Inner Domain Residue Modulates Env Conformation and Trimer Stability.

Ding, S.Tolbert, W.D.Prevost, J.Pacheco, B.Coutu, M.Debbeche, O.Xiang, S.H.Pazgier, M.Finzi, A.

(2016) J Virol 90: 8395-8409

  • DOI: https://doi.org/10.1128/JVI.01068-16
  • Primary Citation of Related Structures:  
    5KJR

  • PubMed Abstract: 

    Previous studies have shown that highly conserved residues in the inner domain of gp120 are required for HIV-1 envelope glycoprotein (Env) transitions to the CD4-bound conformation (A. Finzi, S. H. Xiang, B. Pacheco, L. Wang, J. Haight, et al., Mol Cell 37:656-667, 2010, http://dx.doi.org/10.1016/j.molcel.2010.02.012; A. Desormeaux, M. Coutu, H. Medjahed, B. Pacheco, A. Herschhorn, et al., J Virol 87:2549-2562, 2013, http://dx.doi.org/10.1128/JVI.03104-12). Moreover, W69, a highly conserved residue located at the interface between layer 1 and layer 2 of the inner domain, was recently shown to be important for efficient Env recognition by CD4-induced (CD4i) antibodies capable of potent antibody-dependent cellular cytotoxicity (W. D. Tolbert, N. Gohain, M. Veillette, J. P. Chapleau, C. Orlandi, et al., 2016, Structure 24:697-709, http://dx.doi.org/10.1016/j.str.2016.03.005; S. Ding, M. Veillette, M. Coutu, J. Prevost, L. Scharf, et al., 2016, J Virol 90:2127-2134, http://dx.doi.org/10.1128/JVI.02779-15). We evaluated the contribution of the hydrophobicity of W69 to conformational changes of Env by replacing it with a series of residues with aliphatic or aromatic side chains of decreasing chain length. We have found that the hydrophobicity of residue 69 is important for Env processing, CD4 binding, and its transition to the CD4-bound conformation. The most deleterious effect was observed when W69 was replaced with alanine or glycine residues. However, the functions lost due to W69 mutations could be progressively restored with amino acids of increasing aliphatic chain length and fully recovered with residues bearing an aromatic ring. Interestingly, poor CD4 binding of W69A could be fully restored by introducing a compensatory mutation within layer 2 (S115W). Structural studies of HIV-1 gp120 coree W69A/S115W mutant bound to the CD4 peptide mimetic M48U1 and Fab of anti-cluster A antibody N60-i3 revealed no perturbations to the overall structure of the double mutant compared to the wild-type protein but identified higher mobility within the interface between layer 1 and layer 2, the bridging sheet region, and the CD4 binding site.IMPORTANCE HIV-1 Env transitions to the CD4-bound conformation are required for viral entry. Previous studies identified a highly conserved residue of the inner domain, W69, as being involved in these conformational transitions (A. Finzi, S. H. Xiang, B. Pacheco, L. Wang, J. Haight, et al., Mol Cell 37:656-667, 2010, http://dx.doi.org/10.1016/j.molcel.2010.02.012). Here, we show that W69, located at the interface between gp120 and gp41 in the PGT151-bound trimer, plays a critical role in the interprotomer signaling induced by CD4 binding. This new information might be useful in immunogen design.


  • Organizational Affiliation

    Centre de Recherche du CHUM, Université de Montréal, Montreal, Quebec, Canada Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
clade A/E 93TH057 HIV-1 gp120 coreA [auth G]353Human immunodeficiency virus 1Mutation(s): 3 
Gene Names: HIV-1 Env
UniProt
Find proteins for A0A0M3KKW9 (Human immunodeficiency virus 1)
Explore A0A0M3KKW9 
Go to UniProtKB:  A0A0M3KKW9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0M3KKW9
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
M48U1 CD4 MIMETIC PEPTIDEB [auth N]28synthetic constructMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
N60-I3 FAB HEAVY CHAINC [auth H]229Homo sapiensMutation(s): 0 
Gene Names: FAB HEAVY CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-I3
Entity Groups  
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
N60-I3 FAB LIGHT CHAIND [auth L]221Homo sapiensMutation(s): 0 
Gene Names: FAB LIGHT CHAIN OF ADCC-POTENT ANTI-HIV-1 ANTIBODY N60-I3
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth G]
F [auth G]
G
H [auth G]
I [auth G]
E [auth G],
F [auth G],
G,
H [auth G],
I [auth G],
J [auth G],
K [auth G],
L [auth G],
M [auth G],
N [auth G]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
O [auth L](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
U2X
Query on U2X
B [auth N]L-PEPTIDE LINKINGC16 H23 N O3TYR
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.249 
  • R-Value Observed: 0.252 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.191α = 90
b = 101.944β = 90
c = 108.747γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI116274

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-20
    Type: Initial release
  • Version 1.1: 2016-09-21
    Changes: Database references
  • Version 1.2: 2016-10-26
    Changes: Structure summary
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Derived calculations
  • Version 1.4: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.6: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.7: 2023-11-15
    Changes: Data collection