6URI

HIV-1 Nef in complex with the CD4 cytoplasmic domain and the AP2 clathrin adaptor complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 

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This is version 1.3 of the entry. See complete history


Literature

Structural basis of CD4 downregulation by HIV-1 Nef.

Kwon, Y.Kaake, R.M.Echeverria, I.Suarez, M.Karimian Shamsabadi, M.Stoneham, C.Ramirez, P.W.Kress, J.Singh, R.Sali, A.Krogan, N.Guatelli, J.Jia, X.

(2020) Nat Struct Mol Biol 27: 822-828

  • DOI: https://doi.org/10.1038/s41594-020-0463-z
  • Primary Citation of Related Structures:  
    6URI

  • PubMed Abstract: 

    The HIV-1 Nef protein suppresses multiple immune surveillance mechanisms to promote viral pathogenesis and is an attractive target for the development of novel therapeutics. A key function of Nef is to remove the CD4 receptor from the cell surface by hijacking clathrin- and adaptor protein complex 2 (AP2)-dependent endocytosis. However, exactly how Nef does this has been elusive. Here, we describe the underlying mechanism as revealed by a 3.0-Å crystal structure of a fusion protein comprising Nef and the cytoplasmic domain of CD4 bound to the tetrameric AP2 complex. An intricate combination of conformational changes occurs in both Nef and AP2 to enable CD4 binding and downregulation. A pocket on Nef previously identified as crucial for recruiting class I MHC is also responsible for recruiting CD4, revealing a potential approach to inhibit two of Nef's activities and sensitize the virus to immune clearance.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, Dartmouth, MA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit alpha641Rattus norvegicusMutation(s): 0 
Gene Names: Ap2a2
UniProt
Find proteins for P18484 (Rattus norvegicus)
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UniProt GroupP18484
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit sigmaB [auth S]142Homo sapiensMutation(s): 0 
Gene Names: AP2S1AP17CLAPS2
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Find proteins for P53680 (Homo sapiens)
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PHAROS:  P53680
GTEx:  ENSG00000042753 
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UniProt GroupP53680
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein NefC [auth N]186Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: nef
UniProt
Find proteins for P03406 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit betaD [auth B]615Homo sapiensMutation(s): 3 
Gene Names: AP2B1ADTB2CLAPB1
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Find proteins for P63010 (Homo sapiens)
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PHAROS:  P63010
GTEx:  ENSG00000006125 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
AP-2 complex subunit muE [auth M]135Homo sapiensMutation(s): 0 
Gene Names: AP2M1CLAPM1KIAA0109
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PHAROS:  Q96CW1
GTEx:  ENSG00000161203 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4F [auth D]62Homo sapiensMutation(s): 0 
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Find proteins for P01730 (Homo sapiens)
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PHAROS:  P01730
GTEx:  ENSG00000010610 
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.242 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.154α = 90
b = 109.154β = 90
c = 178.915γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references
  • Version 1.2: 2020-09-23
    Changes: Database references
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description