4NEE

crystal structure of AP-2 alpha/simga2 complex bound to HIV-1 Nef


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

How HIV-1 Nef hijacks the AP-2 clathrin adaptor to downregulate CD4.

Ren, X.Park, S.Y.Bonifacino, J.S.Hurley, J.H.

(2014) Elife 3: e01754-e01754

  • DOI: https://doi.org/10.7554/eLife.01754
  • Primary Citation of Related Structures:  
    4NEE

  • PubMed Abstract: 

    The Nef protein of HIV-1 downregulates the cell surface co-receptor CD4 by hijacking the clathrin adaptor complex AP-2. The structural basis for the hijacking of AP-2 by Nef is revealed by a 2.9 Å crystal structure of Nef bound to the α and σ2 subunits of AP-2. Nef binds to AP-2 via its central loop (residues 149-179) and its core. The determinants for Nef binding include residues that directly contact AP-2 and others that stabilize the binding-competent conformation of the central loop. Residues involved in both direct and indirect interactions are required for the binding of Nef to AP-2 and for downregulation of CD4. These results lead to a model for the docking of the full AP-2 tetramer to membranes as bound to Nef, such that the cytosolic tail of CD4 is situated to interact with its binding site on Nef. DOI: http://dx.doi.org/10.7554/eLife.01754.001.


  • Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit sigmaA [auth D],
B [auth L],
C [auth F],
D [auth I]
142Rattus norvegicusMutation(s): 0 
Gene Names: Ap2s1Ap17Claps2
UniProt
Find proteins for P62744 (Rattus norvegicus)
Explore P62744 
Go to UniProtKB:  P62744
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62744
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit alpha-2E [auth G],
F [auth B],
G [auth J],
H [auth A]
398Rattus norvegicusMutation(s): 0 
Gene Names: Ap17Ap2a2Ap2s1Claps2
UniProt
Find proteins for P18484 (Rattus norvegicus)
Explore P18484 
Go to UniProtKB:  P18484
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18484
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein NefI [auth E],
J [auth H],
K,
L [auth C]
155Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: nef
UniProt
Find proteins for P04601 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04601 
Go to UniProtKB:  P04601
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04601
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.558α = 90
b = 168.034β = 90
c = 200.204γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-03-05
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Refinement description