5NUH

Crystal structure of SIVmac239 Nef bound to an engineered Hck SH3 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Endocytic sorting motif interactions involved in Nef-mediated downmodulation of CD4 and CD3.

Manrique, S.Sauter, D.Horenkamp, F.A.Lulf, S.Yu, H.Hotter, D.Anand, K.Kirchhoff, F.Geyer, M.

(2017) Nat Commun 8: 442-442

  • DOI: 10.1038/s41467-017-00481-z
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lentiviral Nefs recruit assembly polypeptide complexes and target sorting motifs in cellular receptors to induce their internalization. While Nef-mediated CD4 downmodulation is conserved, the ability to internalize CD3 was lost in HIV-1 and its precu ...

    Lentiviral Nefs recruit assembly polypeptide complexes and target sorting motifs in cellular receptors to induce their internalization. While Nef-mediated CD4 downmodulation is conserved, the ability to internalize CD3 was lost in HIV-1 and its precursors. Although both functions play key roles in lentiviral replication and pathogenicity, the underlying structural requirements are poorly defined. Here, we determine the structure of SIVmac239 Nef bound to the ExxxLM motif of another Nef molecule at 2.5 Å resolution. This provides a basis for a structural model, where a hydrophobic crevice in simian immunodeficiency virus (SIV) Nef targets a dileucine motif in CD4 and a tyrosine-based motif in CD3. Introducing key residues into this crevice of HIV-1 Nef enables CD3 binding but an additional N-terminal tyrosine motif is required for internalization. Our resolution of the CD4/Nef/AP2 complex and generation of HIV-1 Nefs capable of CD3 downregulation provide insights into sorting motif interactions and target discrimination of Nef.HIV and simian immunodeficiency virus (SIV) Nef proteins both stimulate the clathrin-mediated endocytosis of CD4 but differ in downmodulation of the immune receptor CD3. Here, the authors present the structure of SIV Nef bound to the ExxxLM motif of another Nef molecule, which allows them to propose a model how Nef recognizes these motifs in CD3 and CD4.


    Organizational Affiliation

    Institute of Innate Immunity, Department of Structural Immunology, University of Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein Nef
A, B
172Simian immunodeficiency virusMutation(s): 0 
Gene Names: nef
Find proteins for Q5QGG3 (Simian immunodeficiency virus)
Go to UniProtKB:  Q5QGG3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein kinase HCK,Tyrosine-protein kinase HCK
C, D
60Homo sapiensMutation(s): 0 
Gene Names: HCK
EC: 2.7.10.2
Find proteins for P08631 (Homo sapiens)
Go to Gene View: HCK
Go to UniProtKB:  P08631
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 104.000α = 90.00
b = 104.000β = 90.00
c = 53.000γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGE 976/6-1

Revision History 

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-13
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Database references