6K6N

Crystal structure of SIVmac239 Nef protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of HIV-2 Nef Reveals Features Distinct from HIV-1 Involved in Immune Regulation.

Hirao, K.Andrews, S.Kuroki, K.Kusaka, H.Tadokoro, T.Kita, S.Ose, T.Rowland-Jones, S.L.Maenaka, K.

(2020) iScience 23: 100758-100758

  • DOI: https://doi.org/10.1016/j.isci.2019.100758
  • Primary Citation of Related Structures:  
    6K6M, 6K6N

  • PubMed Abstract: 

    The human immunodeficiency virus (HIV) accessory protein Nef plays a major role in establishing and maintaining infection, particularly through immune evasion. Many HIV-2-infected people experience long-term viral control and survival, resembling HIV-1 elite control. HIV-2 Nef has overlapping but also distinct functions from HIV-1 Nef. Here we report the crystal structure of HIV-2 Nef core. The di-leucine sorting motif forms a helix bound to neighboring molecules, and moreover, isothermal titration calorimetry demonstrated that the CD3 endocytosis motif can directly bind to HIV-2 Nef, ensuring AP-2-mediated endocytosis for CD3. The highly conserved C-terminal region forms a α-helix, absent from HIV-1. We further determined the structure of simian immunodeficiency virus (SIV) Nef harboring this region, demonstrating similar C-terminal α-helix, which may contribute to AP-1 binding for MHC-I downregulation. These results provide insights into the distinct pathogenesis of HIV-2 infection.


  • Organizational Affiliation

    Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0812, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein Nef176Simian immunodeficiency virusMutation(s): 0 
Gene Names: nef
UniProt
Find proteins for Q203Y4 (Simian immunodeficiency virus)
Explore Q203Y4 
Go to UniProtKB:  Q203Y4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ203Y4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.531α = 90
b = 72.531β = 90
c = 111.087γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan15H02384
Japan Society for the Promotion of ScienceJapan22121007
Japan Society for the Promotion of ScienceJapanStrategic Young Researcher Overseas Visits Program for Accelerating Brain Circulation
Japan Agency for Medical Research and Development (AMED)Japan18am0101093j0002
Japan Agency for Medical Research and Development (AMED)Japan18ae0101047h
Japan Science and TechnologyJapanSupport Program for Implementation of New Equipment Sharing System

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-25
    Type: Initial release
  • Version 1.1: 2021-04-21
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description