4NEE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8841 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.7554/eLife.01754

  • 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 subuni ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AP-2 complex subunit sigma
D, L, F, I
142Rattus norvegicusMutation(s): 0 
Gene Names: Ap2s1 (Ap17, Claps2)
Find proteins for P62744 (Rattus norvegicus)
Go to UniProtKB:  P62744
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AP-2 complex subunit alpha-2
G, B, J, A
398Rattus norvegicusMutation(s): 0 
Gene Names: Ap2a2 (Adtab)
Find proteins for P18484 (Rattus norvegicus)
Go to UniProtKB:  P18484
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Protein Nef
E, H, K, C
155Human immunodeficiency virus type 1 group M subtype BMutation(s): 0 
Gene Names: nef
Find proteins for P04601 (Human immunodeficiency virus type 1 group M subtype B)
Go to UniProtKB:  P04601
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
C, E, H, K
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8841 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 109.558α = 90.00
b = 168.034β = 90.00
c = 200.204γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-03-05
    Type: Database references