4P6Z

Crystal structure of the human BST2 cytoplasmic domain and the HIV-1 Vpu cytoplasmic domain bound to the clathrin adaptor protein complex 1 (AP1) core

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Structural basis of HIV-1 Vpu-mediated BST2 antagonism via hijacking of the clathrin adaptor protein complex 1.

Jia, X., Weber, E., Tokarev, A., Lewinski, M., Rizk, M., Suarez, M., Guatelli, J., Xiong, Y.

(2014) Elife 3: e02362-e02362

  • DOI: 10.7554/eLife.02362
  • Primary Citation of Related Structures:  
    4P6Z

  • PubMed Abstract: 

    • BST2/tetherin, an antiviral restriction factor, inhibits the release of enveloped viruses from the cell surface. Human immunodeficiency virus-1 (HIV-1) antagonizes BST2 through viral protein u (Vpu), which downregulates BST2 from the cell surface. We report the crystal structure of a protein complex containing Vpu and BST2 cytoplasmic domains and the core of the clathrin adaptor protein complex 1 (AP1) ...

    BST2/tetherin, an antiviral restriction factor, inhibits the release of enveloped viruses from the cell surface. Human immunodeficiency virus-1 (HIV-1) antagonizes BST2 through viral protein u (Vpu), which downregulates BST2 from the cell surface. We report the crystal structure of a protein complex containing Vpu and BST2 cytoplasmic domains and the core of the clathrin adaptor protein complex 1 (AP1). This, together with our biochemical and functional validations, reveals how Vpu hijacks the AP1-dependent membrane trafficking pathways to mistraffick BST2. Vpu mimics a canonical acidic dileucine-sorting motif to bind AP1 in the cytosol, while simultaneously interacting with BST2 in the membrane. These interactions enable Vpu to build on an intrinsic interaction between BST2 and AP1, presumably causing the observed retention of BST2 in juxtanuclear endosomes and stimulating its degradation in lysosomes. The ability of Vpu to hijack AP-dependent trafficking pathways suggests a potential common theme for Vpu-mediated downregulation of host proteins.DOI: http://dx.doi.org/10.7554/eLife.02362.001.

    Organizational Affiliation: 

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States yong.xiong@yale.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit gamma-1A [auth G]627Mus musculusMutation(s): 0 
Gene Names: Ap1g1, Adtg, Clapg1
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IMPC:  MGI:101919
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UniProt GroupP22892
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit sigma-1AB [auth S]158Homo sapiensMutation(s): 1 
Gene Names: AP1S1, AP19, CLAPS1
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Find proteins for P61966 (Homo sapiens)
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PHAROS:  P61966
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit mu-1C [auth M]423Mus musculusMutation(s): 0 
Gene Names: Ap1m1, Cltnm
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Find proteins for P35585 (Mus musculus)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
AP-1 complex subunit beta-1D [auth B]600Homo sapiensMutation(s): 2 
Gene Names: AP1B1, ADTB1, BAM22, CLAPB2
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Protein VpuE [auth V]63Human immunodeficiency virus type 1 (SF162 ISOLATE)Mutation(s): 0 
Gene Names: vpu
UniProt
Find proteins for P19554 (Human immunodeficiency virus type 1 group M subtype B (isolate SF162))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Bone marrow stromal antigen 2F [auth T]25Homo sapiensMutation(s): 0 
Gene Names: BST2
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PHAROS:  Q10589
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 160.536α = 90
b = 160.536β = 90
c = 118.393γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data scaling
PHASERphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2014-03-25 
  • Released Date: 2014-05-21 
    • Deposition Author(s): Jia, X., Xiong, Y.
Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI102778
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI097064
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI081668
The James B. Pendleton Charitable TrustUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence, Derived calculations, Other, Refinement description, Source and taxonomy
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence