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- PDB-3nwh: Crystal structure of BST2/Tetherin -

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Basic information

Entry
Database: PDB / ID: 3nwh
TitleCrystal structure of BST2/Tetherin
ComponentsBone marrow stromal antigen 2
KeywordsANTIVIRAL PROTEIN / Coiled-coil / innate immunity
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 / positive regulation of leukocyte proliferation / azurophil granule membrane / negative regulation of viral genome replication / B cell activation / response to type II interferon ...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 / positive regulation of leukocyte proliferation / azurophil granule membrane / negative regulation of viral genome replication / B cell activation / response to type II interferon / side of membrane / multivesicular body / negative regulation of cell migration / regulation of actin cytoskeleton organization / response to virus / negative regulation of cell growth / SARS-CoV-1 activates/modulates innate immune responses / Interferon alpha/beta signaling / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / membrane raft / apical plasma membrane / intracellular membrane-bounded organelle / innate immune response / Neutrophil degranulation / Golgi apparatus / cell surface / protein homodimerization activity / RNA binding / extracellular exosome / membrane / identical protein binding / 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
Bone marrow stromal antigen 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsSchubert, H.L. / Zhai, Q. / Hill, C.P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural and functional studies on the extracellular domain of BST2/tetherin in reduced and oxidized conformations.
Authors: Schubert, H.L. / Zhai, Q. / Sandrin, V. / Eckert, D.M. / Garcia-Maya, M. / Saul, L. / Sundquist, W.I. / Steiner, R.A. / Hill, C.P.
History
DepositionJul 9, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionJul 21, 2010ID: 3MKX
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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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
C: Bone marrow stromal antigen 2
D: Bone marrow stromal antigen 2


Theoretical massNumber of molelcules
Total (without water)50,4314
Polymers50,4314
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12930 Å2
ΔGint-146 kcal/mol
Surface area26590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)26.550, 59.584, 159.473
Angle α, β, γ (deg.)90.000, 91.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 12607.732 Da / Num. of mol.: 4 / Fragment: Extracellular Domain (UNP residues 47-152)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BST2 / Plasmid: pTOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q10589
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.5 Å3/Da / Density % sol: 50.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.2
Details: PEG MME 2K, pH 7.2, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.9805, 0.9919, 0.9809
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 2, 2009
RadiationMonochromator: side scattering I-beam bent single crystal; asymmetric cut 4.9650 deg
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.98051
20.99191
30.98091
ReflectionRedundancy: 3.6 % / Av σ(I) over netI: 17.18 / Number: 15493 / Rmerge(I) obs: 0.058 / Χ2: 1.05 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 15096 / % possible obs: 97.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.65097.210.0321.0553.9
4.455.697.510.0451.0383.8
3.884.4598.610.0450.9763.9
3.533.8898.210.0561.013.7
3.283.5398.310.0771.0663.7
3.083.2898.610.11.0453.6
2.933.0898.310.1141.0783.6
2.82.9397.210.1341.0613.5
2.692.898.210.2131.0943.4
2.62.6993.210.2691.0823.3
ReflectionResolution: 2.6→50 Å / Num. all: 15493 / Num. obs: 15096 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.058 / Χ2: 1.048 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.6-2.693.30.2693.9827881.08293.2
2.69-2.83.40.21328551.09498.2
2.8-2.933.50.13430201.06197.2
2.93-3.083.60.11428851.07898.3
3.08-3.283.60.130241.04598.6
3.28-3.533.70.07728851.06698.3
3.53-3.883.70.05629851.0198.2
3.88-4.453.90.04529830.97698.6
4.45-5.63.80.04528971.03897.5
5.6-503.90.03229301.05597.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0074refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→33.13 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.916 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 28.516 / SU ML: 0.275 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.346 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2877 1147 7.6 %RANDOM
Rwork0.2601 ---
obs0.2622 15096 97.44 %-
all-15500 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 161.21 Å2 / Biso mean: 56.2268 Å2 / Biso min: 20.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å2-4.46 Å2
2--3.31 Å2-0 Å2
3----2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.6→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3212 0 0 18 3230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0213267
X-RAY DIFFRACTIONr_bond_other_d0.0060.022211
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.9534390
X-RAY DIFFRACTIONr_angle_other_deg2.90335424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3435421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.17325.568176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.68915649
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2941530
X-RAY DIFFRACTIONr_chiral_restr0.0990.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023686
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02584
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.511 81 -
Rwork0.381 949 -
all-1030 -
obs--90.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
110.94810.843715.02420.29911.114520.79930.36380.0167-0.13240.0846-0.0926-0.11530.54260.0981-0.27120.1614-0.03520.09030.3082-0.00710.2711-18.586554.326679.268
216.2251.312418.99680.19931.516322.2689-0.58350.40950.6715-0.176-0.16310.1155-0.60210.44670.74660.36310.09520.04290.6107-0.10430.3752-79.478447.40662.6288
313.78592.927414.6360.76833.140315.5882-0.8092-0.35120.7638-0.1309-0.04820.1255-0.9272-0.30440.85740.299-0.05030.00030.28660.05240.3395-21.797454.654680.9322
49.90532.126514.50750.65193.183221.28040.77510.1456-0.45960.0274-0.14510.05221.12090.1012-0.63010.39210.0112-0.00810.5039-0.03760.3502-81.76547.05225.535
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 151
2X-RAY DIFFRACTION2B48 - 151
3X-RAY DIFFRACTION3C48 - 151
4X-RAY DIFFRACTION4D50 - 150

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