3REB

HIV-1 Nef protein in complex with engineered Hck-SH3 domain

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Molecular design, functional characterization and structural basis of a protein inhibitor against the HIV-1 pathogenicity factor Nef.

Breuer, S., Schievink, S.I., Schulte, A., Blankenfeldt, W., Fackler, O.T., Geyer, M.

(2011) PLoS One 6: e20033-e20033

  • DOI: 10.1371/journal.pone.0020033
  • Primary Citation of Related Structures:  
    3REA, 3REB

  • PubMed Abstract: 

    • Increased spread of HIV-1 and rapid emergence of drug resistance warrants development of novel antiviral strategies. Nef, a critical viral pathogenicity factor that interacts with host cell factors but lacks enzymatic activity, is not targeted by current ...

    Increased spread of HIV-1 and rapid emergence of drug resistance warrants development of novel antiviral strategies. Nef, a critical viral pathogenicity factor that interacts with host cell factors but lacks enzymatic activity, is not targeted by current antiviral measures. Here we inhibit Nef function by simultaneously blocking several highly conserved protein interaction surfaces. This strategy, referred to as "wrapping Nef", is based on structure-function analyses that led to the identification of four target sites: (i) SH3 domain interaction, (ii) interference with protein transport processes, (iii) CD4 binding and (iv) targeting to lipid membranes. Screening combinations of Nef-interacting domains, we developed a series of small Nef interacting proteins (NIs) composed of an SH3 domain optimized for binding to Nef, fused to a sequence motif of the CD4 cytoplasmic tail and combined with a prenylation signal for membrane association. NIs bind to Nef in the low nM affinity range, associate with Nef in human cells and specifically interfere with key biological activities of Nef. Structure determination of the Nef-inhibitor complex reveals the molecular basis for binding specificity. These results establish Nef-NI interfaces as promising leads for the development of potent Nef inhibitors.

    Organizational Affiliation: 

    Abteilung Physikalische Biochemie, Max-Planck-Institut für molekulare Physiologie, Dortmund, Germany.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein Nef A, C166HIV-1 M:B_ARV2/SF2Mutation(s): 4 
Gene Names: HIV-1 Nef, nef
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 HCK B, D90Homo sapiensMutation(s): 6 
Gene Names: HCK
EC: 2.7.10.2
Find proteins for P08631 (Homo sapiens)
Explore P08631 
Go to UniProtKB:  P08631
NIH Common Fund Data Resources
PHAROS:  P08631
GTEx:  ENSG00000101336
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.46α = 90
b = 112.46β = 90
c = 130.03γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-10-10
    Changes: Data collection, Database references, Structure summary