4U5W

Crystal Structure of HIV-1 Nef-SF2 Core Domain in Complex with the Src Family Kinase Hck SH3-SH2 Tandem Regulatory Domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Interaction with the Src Homology (SH3-SH2) Region of the Src-family Kinase Hck Structures the HIV-1 Nef Dimer for Kinase Activation and Effector Recruitment.

Alvarado, J.J.Tarafdar, S.Yeh, J.I.Smithgall, T.E.

(2014) J.Biol.Chem. 289: 28539-28553

  • DOI: 10.1074/jbc.M114.600031

  • PubMed Abstract: 
  • HIV-1 Nef supports high titer viral replication in vivo and is essential for AIDS progression. Nef function depends on interactions with multiple host cell effectors, including Hck and other Src-family kinases. Here we describe the x-ray crystal stru ...

    HIV-1 Nef supports high titer viral replication in vivo and is essential for AIDS progression. Nef function depends on interactions with multiple host cell effectors, including Hck and other Src-family kinases. Here we describe the x-ray crystal structure of Nef in complex with the Hck SH3-SH2 regulatory region to a resolution of 1.86 Å. The complex crystallized as a dimer of complexes, with the conserved Nef PXXPXR motif engaging the Hck SH3 domain. A new intercomplex contact was found between SH3 Glu-93, and Nef Arg-105. Mutagenesis of Hck SH3 Glu-93 interfered with Nef·Hck complex formation and kinase activation in cells. The Hck SH2 domains impinge on the N-terminal region of Nef to stabilize a dimer conformation that exposes Asp-123, a residue critical for Nef function. Our results suggest that in addition to serving as a kinase effector for Nef, Hck binding may reorganize the Nef dimer for functional interaction with other signaling partners.


    Organizational Affiliation

    From the Departments of Microbiology and Molecular Genetics and Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219 and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein Nef
A, C
149Human immunodeficiency virus type 1 group M subtype BGene Names: nef
Find proteins for P03407 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P03407
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase HCK
B, D
180Homo sapiensGene Names: HCK
EC: 2.7.10.2
Find proteins for P08631 (Homo sapiens)
Go to Gene View: HCK
Go to UniProtKB:  P08631
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A, B, C, D
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.169 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 56.489α = 112.28
b = 57.265β = 96.09
c = 72.111γ = 106.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI057083
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI102724
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM082251

Revision History 

  • Version 1.0: 2014-08-20
    Type: Initial release
  • Version 1.1: 2014-08-27
    Type: Database references
  • Version 1.2: 2014-10-22
    Type: Database references
  • Version 1.3: 2017-09-13
    Type: Advisory, Author supporting evidence, Database references, Derived calculations, Other, Source and taxonomy