Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 216.05 kDa 
• Atom Count: 13940 
• Modelled Residue Count: 1740 
• Deposited Residue Count: 1896 
• Unique protein chains: 6

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

• DOI: 10.2210/pdb4P6Z/pdb

• Classification: PROTEIN TRANSPORT
• Organism(s): Mus musculus, Homo sapiens, Human immunodeficiency virus type 1 (SF162 ISOLATE)
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2014-03-25 Released: 2014-05-21 
• Deposition Author(s): Jia, X., Xiong, Y.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), The James B. Pendleton Charitable Trust

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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 

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

• PubMed: 24843023 
• 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). 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.

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Organizational Affiliation: 

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-1 complex subunit gamma-1	A [auth G]	627	Mus musculus	Mutation(s): 0  Gene Names: Ap1g1, Adtg, Clapg1
UniProt & NIH Common Fund Data Resources
Find proteins for P22892 (Mus musculus) Explore P22892  Go to UniProtKB:  P22892
IMPC:  MGI:101919

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-1 complex subunit sigma-1A	B [auth S]	158	Homo sapiens	Mutation(s): 1  Gene Names: AP1S1, AP19, CLAPS1
UniProt & NIH Common Fund Data Resources
Find proteins for P61966 (Homo sapiens) Explore P61966  Go to UniProtKB:  P61966
PHAROS:  P61966 GTEx:  ENSG00000106367

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-1 complex subunit mu-1	C [auth M]	423	Mus musculus	Mutation(s): 0  Gene Names: Ap1m1, Cltnm
UniProt
Find proteins for P35585 (Mus musculus) Explore P35585  Go to UniProtKB:  P35585

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
AP-1 complex subunit beta-1	D [auth B]	600	Homo sapiens	Mutation(s): 2  Gene Names: AP1B1, ADTB1, BAM22, CLAPB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q10567 (Homo sapiens) Explore Q10567  Go to UniProtKB:  Q10567
PHAROS:  Q10567 GTEx:  ENSG00000100280

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Vpu	E [auth V]	63	Human 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)) Explore P19554  Go to UniProtKB:  P19554

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Bone marrow stromal antigen 2	F [auth T]	25	Homo sapiens	Mutation(s): 0  Gene Names: BST2
UniProt & NIH Common Fund Data Resources
Find proteins for Q10589 (Homo sapiens) Explore Q10589  Go to UniProtKB:  Q10589
PHAROS:  Q10589 GTEx:  ENSG00000130303

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 = 160.536	α = 90
b = 160.536	β = 90
c = 118.393	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
HKL-2000	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2014-03-25 
• Released Date: 2014-05-21 
Deposition Author(s): Jia, X., Xiong, Y.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI102778
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI097064
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI081668
The James B. Pendleton Charitable Trust	United States	--

Revision History  

• 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