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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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 

  • DOI: 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 ...

    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. xjia@umassd.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AP-2 complex subunit alphaA641Rattus norvegicusMutation(s): 0 
Gene Names: Ap2a2
Find proteins for Q66HM2 (Rattus norvegicus)
Explore Q66HM2 
Go to UniProtKB:  Q66HM2
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AP-2 complex subunit sigmaS142Homo sapiensMutation(s): 0 
Gene Names: AP2S1AP17CLAPS2
Find proteins for P53680 (Homo sapiens)
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Go to UniProtKB:  P53680
NIH Common Fund Data Resources
PHAROS  P53680
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
AP-2 complex subunit muM135Homo sapiensMutation(s): 0 
Gene Names: AP2M1CLAPM1KIAA0109
Find proteins for Q96CW1 (Homo sapiens)
Explore Q96CW1 
Go to UniProtKB:  Q96CW1
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PHAROS  Q96CW1
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Protein NefN186Human immunodeficiency virus 1Mutation(s): 0 
Gene Names: nef
Find proteins for Q90VU7 (Human immunodeficiency virus 1)
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Go to UniProtKB:  Q90VU7
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
AP-2 complex subunit betaB615Homo sapiensMutation(s): 3 
Gene Names: AP2B1ADTB2CLAPB1
Find proteins for P63010 (Homo sapiens)
Explore P63010 
Go to UniProtKB:  P63010
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PHAROS  P63010
Protein Feature View
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  • Reference Sequence
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
cDNA FLJ50658, highly similar to T-cell surface glycoprotein CD4D62Homo sapiensMutation(s): 0 
Find proteins for B4DT49 (Homo sapiens)
Explore B4DT49 
Go to UniProtKB:  B4DT49
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  • Reference Sequence
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

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2019-10-23 
  • Released Date: 2020-07-29 
  • Deposition Author(s): Jia, X., Kwon, Y.

Revision History 

  • Version 1.0: 2020-07-29
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references