3NWH | pdb_00003nwh

Crystal structure of BST2/Tetherin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.288 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.260 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 
    0.262 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3NWH

This is version 1.3 of the entry. See complete history

Literature

Structural and functional studies on the extracellular domain of BST2/tetherin in reduced and oxidized conformations.

Schubert, H.L.Zhai, Q.Sandrin, V.Eckert, D.M.Garcia-Maya, M.Saul, L.Sundquist, W.I.Steiner, R.A.Hill, C.P.

(2010) Proc Natl Acad Sci U S A 107: 17951-17956

  • DOI: https://doi.org/10.1073/pnas.1008206107
  • Primary Citation Related Structures: 
    2XG7, 3NWH

  • PubMed Abstract: 

    HIV-1 and other enveloped viruses can be restricted by a host cellular protein called BST2/tetherin that prevents release of budded viruses from the cell surface. Mature BST2 contains a small cytosolic region, a predicted transmembrane helix, and an extracellular domain with a C-terminal GPI anchor. To advance understanding of BST2 function, we have determined a 2.6 Å crystal structure of the extracellular domain of the bacterially expressed recombinant human protein, residues 47-152, under reducing conditions. The structure forms a single long helix that associates as a parallel dimeric coiled coil over its C-terminal two-thirds, while the N-terminal third forms an antiparallel four-helix bundle with another dimer, creating a global tetramer. We also report the 3.45 Å resolution structure of BST2(51-151) prepared by expression as a secreted protein in HEK293T cells. This oxidized construct forms a dimer in the crystal that is superimposable with the reduced protein over the C-terminal two-thirds of the molecule, and its N terminus suggests pronounced flexibility. Hydrodynamic data demonstrated that BST2 formed a stable tetramer under reducing conditions and a dimer when oxidized to form disulfide bonds. A mutation that selectively disrupted the tetramer (L70D) increased protein expression modestly but only reduced antiviral activity by approximately threefold. Our data raise the possibility that BST2 may function as a tetramer at some stage, such as during trafficking, and strongly support a model in which the primary functional state of BST2 is a parallel disulfide-bound coiled coil that displays flexibility toward its N terminus.


  • Organizational Affiliation
    • Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112-5650, USA.

Macromolecule Content 

  • Total Structure Weight: 50.43 kDa 
  • Atom Count: 3,266 
  • Modeled Residue Count: 415 
  • Deposited Residue Count: 448 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Bone marrow stromal antigen 2
A, B, C, D
112Homo sapiensMutation(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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ10589
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.288 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.260 (Depositor), 0.253 (DCC) 
  • R-Value Observed: 0.262 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 26.55α = 90
b = 59.584β = 91.56
c = 159.473γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary