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- PDB-3ni0: Crystal Structure of Mouse BST-2/Tetherin Ectodomain -

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Basic information

Entry
Database: PDB / ID: 3ni0
TitleCrystal Structure of Mouse BST-2/Tetherin Ectodomain
ComponentsBone marrow stromal antigen 2
KeywordsIMMUNE SYSTEM / coiled-coil / antiviral defense / GPI anchor
Function / homology
Function and homology information


negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / response to interferon-alpha / metalloendopeptidase inhibitor activity / negative regulation of viral genome replication / response to type II interferon / side of membrane / Neutrophil degranulation / negative regulation of cell migration ...negative regulation of plasmacytoid dendritic cell cytokine production / negative regulation of intracellular transport of viral material / response to interferon-beta / response to interferon-alpha / metalloendopeptidase inhibitor activity / negative regulation of viral genome replication / response to type II interferon / side of membrane / Neutrophil degranulation / negative regulation of cell migration / regulation of actin cytoskeleton organization / response to virus / negative regulation of cell growth / late endosome / defense response to virus / membrane raft / apical plasma membrane / innate immune response / Golgi apparatus / cell surface / plasma membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1700 / Bone marrow stromal antigen 2 / Bone marrow stromal antigen 2 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Bone marrow stromal antigen 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 Å
AuthorsScheaffer, S.M. / Brett, T.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Biophysical Analysis of BST-2/Tetherin Ectodomains Reveals an Evolutionary Conserved Design to Inhibit Virus Release.
Authors: Swiecki, M. / Scheaffer, S.M. / Allaire, M. / Fremont, D.H. / Colonna, M. / Brett, T.J.
History
DepositionJun 14, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bone marrow stromal antigen 2
B: Bone marrow stromal antigen 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4433
Polymers22,3832
Non-polymers601
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-44 kcal/mol
Surface area13900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.685, 100.831, 110.432
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-253-

HOH

21B-254-

HOH

31B-267-

HOH

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Components

#1: Protein Bone marrow stromal antigen 2 / BST-2 / HM1.24 antigen / CD317


Mass: 11191.465 Da / Num. of mol.: 2 / Fragment: UNP residues 53-151
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bst2 / Plasmid: pET23B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) codon plus / References: UniProt: Q8R2Q8
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.28 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M phosphate/citrate, 35% isopropanol, 5% PEG 1000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00007 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jun 24, 2009 / Details: Mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00007 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 25314 / Num. obs: 25314 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 28
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2465 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1D7M

1d7m


Resolution: 1.601→32.154 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 1196 5.06 %random
Rwork0.2138 ---
obs0.2149 23628 93.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.095 Å2 / ksol: 0.445 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7543 Å20 Å2-0 Å2
2--9.3017 Å20 Å2
3----11.056 Å2
Refinement stepCycle: LAST / Resolution: 1.601→32.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1452 0 4 225 1681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031459
X-RAY DIFFRACTIONf_angle_d0.5641959
X-RAY DIFFRACTIONf_dihedral_angle_d14.348580
X-RAY DIFFRACTIONf_chiral_restr0.033241
X-RAY DIFFRACTIONf_plane_restr0.001262
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.601-1.66530.27621220.22162291241387
1.6653-1.74110.2711200.22132301242188
1.7411-1.83290.25521350.21112276241187
1.8329-1.94770.25031220.21972352247489
1.9477-2.09810.22841350.19912614274998
2.0981-2.30920.22431230.19262584270797
2.3092-2.64320.19981400.19422632277298
2.6432-3.32960.23371660.20812645281199
3.3296-32.16050.24731330.23092737287096

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