7D7S

HIV-1 SF2 Nef in complex with the Fyn SH3 R96I mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.288 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Synergy and allostery in ligand binding by HIV-1 Nef.

Aldehaiman, A.Momin, A.A.Restouin, A.Wang, L.Shi, X.Aljedani, S.Opi, S.Lugari, A.Shahul Hameed, U.F.Ponchon, L.Morelli, X.Huang, M.Dumas, C.Collette, Y.Arold, S.T.

(2021) Biochem J 478: 1525-1545

  • DOI: 10.1042/BCJ20201002
  • Primary Citation of Related Structures:  
    7D7S

  • PubMed Abstract: 
  • The Nef protein of human and simian immunodeficiency viruses boosts viral pathogenicity through its interactions with host cell proteins. By combining the polyvalency of its large unstructured regions with the binding selectivity and strength of its folded core domain, Nef can associate with many different host cell proteins, thereby disrupting their functions ...

    The Nef protein of human and simian immunodeficiency viruses boosts viral pathogenicity through its interactions with host cell proteins. By combining the polyvalency of its large unstructured regions with the binding selectivity and strength of its folded core domain, Nef can associate with many different host cell proteins, thereby disrupting their functions. For example, the combination of a linear proline-rich motif and hydrophobic core domain surface allows Nef to bind tightly and specifically to SH3 domains of Src family kinases. We investigated whether the interplay between Nef's flexible regions and its core domain could allosterically influence ligand selection. We found that the flexible regions can associate with the core domain in different ways, producing distinct conformational states that alter the way in which Nef selects for SH3 domains and exposes some of its binding motifs. The ensuing crosstalk between ligands might promote functionally coherent Nef-bound protein ensembles by synergizing certain subsets of ligands while excluding others. We also combined proteomic and bioinformatics analyses to identify human proteins that select SH3 domains in the same way as Nef. We found that only 3% of clones from a whole-human fetal library displayed Nef-like SH3 selectivity. However, in most cases, this selectivity appears to be achieved by a canonical linear interaction rather than by a Nef-like 'tertiary' interaction. Our analysis supports the contention that Nef's mode of hijacking SH3 domains is a virus-specific adaptation with no or very few cellular counterparts. Thus, the Nef tertiary binding surface is a promising virus-specific drug target.


    Organizational Affiliation

    Centre de Biochimie Structurale, CNRS, INSERM, Université de Montpellier, 34090 Montpellier, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein NefA, B223HIV-1 M:B_ARV2/SF2Mutation(s): 0 
Gene Names: nef
UniProt
Find proteins for P03407 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2))
Explore P03407 
Go to UniProtKB:  P03407
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein kinase FynC, D72Homo sapiensMutation(s): 1 
Gene Names: FYN
UniProt & NIH Common Fund Data Resources
Find proteins for E5RFS5 (Homo sapiens)
Explore E5RFS5 
Go to UniProtKB:  E5RFS5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.32 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.286 
  • R-Value Observed: 0.288 
  • Space Group: P 64 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.11α = 90
b = 122.11β = 90
c = 145.89γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2021-06-02
    Changes: Database references