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 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 

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

  • 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 ...

    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.,Department of Medicine, University of California San Diego, La Jolla, United States The VA San Diego Healthcare System, San Diego, United States.,Department of Medicine, University of California San Diego, La Jolla, United States The VA San Diego Healthcare System, San Diego, United States jguatelli@ucsd.edu.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AP-1 complex subunit gamma-1
G
627Mus musculusMutation(s): 0 
Gene Names: Ap1g1 (Adtg, Clapg1)
Find proteins for P22892 (Mus musculus)
Go to UniProtKB:  P22892
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AP-1 complex subunit sigma-1A
S
158Homo sapiensMutation(s): 1 
Gene Names: AP1S1 (AP19, CLAPS1)
Find proteins for P61966 (Homo sapiens)
Go to Gene View: AP1S1
Go to UniProtKB:  P61966
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
AP-1 complex subunit mu-1
M
423Mus musculusMutation(s): 0 
Gene Names: Ap1m1 (Cltnm)
Find proteins for P35585 (Mus musculus)
Go to UniProtKB:  P35585
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
AP-1 complex subunit beta-1
B
600Homo sapiensMutation(s): 2 
Gene Names: AP1B1 (ADTB1, BAM22, CLAPB2)
Find proteins for Q10567 (Homo sapiens)
Go to Gene View: AP1B1
Go to UniProtKB:  Q10567
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
Protein Vpu
V
63Human immunodeficiency virus type 1 group M subtype B (isolate SF162)Mutation(s): 0 
Gene Names: vpu
Find proteins for P19554 (Human immunodeficiency virus type 1 group M subtype B (isolate SF162))
Go to UniProtKB:  P19554
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
Bone marrow stromal antigen 2
T
25Homo sapiensMutation(s): 0 
Gene Names: BST2
Find proteins for Q10589 (Homo sapiens)
Go to Gene View: BST2
Go to UniProtKB:  Q10589
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.186 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 160.536α = 90.00
b = 160.536β = 90.00
c = 118.393γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
CBASSdata collection
HKL-2000data scaling
Cootmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots


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 

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