9A0E | pdb_00009a0e

Structural basis of CD4 downregulation by HIV-1 Nef

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.


Integrative Structure Snapshot

  • Multi-Scale: Yes 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 1 
  • Representative Model: 1 

This is version 1.0 of the entry. See complete history


Literature

Structural basis of CD4 downregulation by HIV-1 Nef.

Kwon YKaake RMEcheverria ISuarez MKarimian Shamsabadi MStoneham CRamirez PWKress JSingh RSali AKrogan NGuatelli JJia 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, 9A0E

  • 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
Nef202Human immunodeficiency virus type 1Mutation(s): 0 
Gene Names: nef
UniProt
Find proteins for Q90VU7 (Human immunodeficiency virus type 1)
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Go to UniProtKB:  Q90VU7
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UniProt GroupQ90VU7
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CD4mut26Homo sapiensMutation(s): 2 
Gene Names: CD4
UniProt & NIH Common Fund Data Resources
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PHAROS:  P01730
GTEx:  ENSG00000010610 
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UniProt GroupP01730
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
AP2alpha2627Rattus 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: 4
MoleculeChains Sequence LengthOrganismDetailsImage
AP2mu2135Homo sapiensMutation(s): 0 
Gene Names: AP2M1
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PHAROS:  Q96CW1
GTEx:  ENSG00000161203 
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UniProt GroupQ96CW1
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
AP2sigma142Homo sapiensMutation(s): 0 
Gene Names: AP2S1
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PHAROS:  P53680
GTEx:  ENSG00000042753 
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UniProt GroupP53680
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
AP2beta2591Homo sapiensMutation(s): 3 
Gene Names: AP2B1
UniProt & NIH Common Fund Data Resources
Find proteins for P63010 (Homo sapiens)
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PHAROS:  P63010
GTEx:  ENSG00000006125 
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Experimental Data & Validation

Integrative Structure Snapshot

  • Multi-Scale: Yes 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 1 
  • Representative Model: 1 

Structure Validation

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View Summary Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-14
    Type: Initial release