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 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/s41467-017-00481-z
  • Primary Citation of Related Structures:  
    5NUH, 5NUI

  • 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 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 SIV mac239 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 Molecular Virology, Ulm University Medical Center, Meyerhofstr. 1, 89081, Ulm, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Nef
A, B
172Simian immunodeficiency virusMutation(s): 0 
Gene Names: nef
UniProt
Find proteins for Q5QGG3 (Simian immunodeficiency virus)
Explore Q5QGG3 
Go to UniProtKB:  Q5QGG3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5QGG3
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tyrosine-protein kinase HCK,Tyrosine-protein kinase HCK
C, D
60Homo sapiensMutation(s): 0 
Gene Names: HCK
EC: 2.7.10.2
UniProt & NIH Common Fund Data Resources
Find proteins for P08631 (Homo sapiens)
Explore P08631 
Go to UniProtKB:  P08631
GTEx:  ENSG00000101336 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08631
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.78 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104α = 90
b = 104β = 90
c = 53γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyGE 976/6-1

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-16
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description