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- PDB-3mq7: Crystal Structure of Ectodomain Mutant of BST-2/Tetherin/CD317 -

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Basic information

Entry
Database: PDB / ID: 3mq7
TitleCrystal Structure of Ectodomain Mutant of BST-2/Tetherin/CD317
ComponentsBone marrow stromal antigen 2
KeywordsANTIVIRAL PROTEIN / HIV
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 / apical plasma membrane / membrane raft / intracellular membrane-bounded organelle / innate immune response / Neutrophil degranulation / cell surface / Golgi apparatus / protein homodimerization activity / RNA binding / extracellular exosome / identical protein binding / membrane / 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: 2.28 Å
AuthorsXiong, Y. / Yang, H. / Wang, J. / Meng, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural insight into the mechanisms of enveloped virus tethering by tetherin.
Authors: Yang, H. / Wang, J. / Jia, X. / McNatt, M.W. / Zang, T. / Pan, B. / Meng, W. / Wang, H.W. / Bieniasz, P.D. / Xiong, Y.
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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
E: Bone marrow stromal antigen 2
F: Bone marrow stromal antigen 2
G: Bone marrow stromal antigen 2
H: Bone marrow stromal antigen 2
I: Bone marrow stromal antigen 2
J: Bone marrow stromal antigen 2
K: Bone marrow stromal antigen 2
L: Bone marrow stromal antigen 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,69714
Polymers162,61712
Non-polymers802
Water2,378132
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44790 Å2
ΔGint-395 kcal/mol
Surface area70270 Å2
MethodPISA
2
A: Bone marrow stromal antigen 2
B: Bone marrow stromal antigen 2
C: Bone marrow stromal antigen 2
D: Bone marrow stromal antigen 2

I: Bone marrow stromal antigen 2
J: Bone marrow stromal antigen 2
K: Bone marrow stromal antigen 2
L: Bone marrow stromal antigen 2
hetero molecules

E: Bone marrow stromal antigen 2
F: Bone marrow stromal antigen 2
G: Bone marrow stromal antigen 2
H: Bone marrow stromal antigen 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,69714
Polymers162,61712
Non-polymers802
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
crystal symmetry operation2_657-x+1,y+1/2,-z+21
Buried area42730 Å2
ΔGint-399 kcal/mol
Surface area72340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.004, 97.156, 117.404
Angle α, β, γ (deg.)90.00, 105.86, 90.00
Int Tables number4
Space group name H-MP1211
Details1

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Components

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


Mass: 13551.396 Da / Num. of mol.: 12 / Fragment: residues 47-161 / Mutation: C53A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BST2 / Plasmid: pMAT9s / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q10589
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: Crystals were grown using the microbatch under-oil method by mixing protein with crystallization buffer containing 200 mM CaCl2, 100 mM HEPEs (pH 7.5), 28% PEG 400. Crystallization under ...Details: Crystals were grown using the microbatch under-oil method by mixing protein with crystallization buffer containing 200 mM CaCl2, 100 mM HEPEs (pH 7.5), 28% PEG 400. Crystallization under oil, pH 7.5, EVAPORATION, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X29A10.9791
SYNCHROTRONNSLS X29A20.9793
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 1, 2010
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97931
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.893
11-H, -K, H+L20.107
ReflectionResolution: 2.28→39 Å / Num. all: 224181 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.07 / Redundancy: 1.9 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 10.6
Reflection shellResolution: 2.28→2.38 Å / Rmerge(I) obs: 0.721 / Mean I/σ(I) obs: 1.07 / Rsym value: 0.721 / % possible all: 89.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.28→38.68 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 13.689 / SU ML: 0.143 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27017 3093 5 %RANDOM
Rwork0.23559 ---
obs0.23736 59073 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.535 Å2
Baniso -1Baniso -2Baniso -3
1-74.44 Å20 Å22.81 Å2
2---3.66 Å20 Å2
3----70.78 Å2
Refinement stepCycle: LAST / Resolution: 2.28→38.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9180 0 2 132 9314
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0219216
X-RAY DIFFRACTIONr_bond_other_d0.0010.026144
X-RAY DIFFRACTIONr_angle_refined_deg1.3991.95312384
X-RAY DIFFRACTIONr_angle_other_deg1.335315060
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.74551176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.05125.61492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.443151788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5511584
X-RAY DIFFRACTIONr_chiral_restr0.0720.21464
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210392
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021644
X-RAY DIFFRACTIONr_mcbond_it3.99765880
X-RAY DIFFRACTIONr_mcbond_other0.98262412
X-RAY DIFFRACTIONr_mcangle_it6.17199324
X-RAY DIFFRACTIONr_scbond_it8.96293336
X-RAY DIFFRACTIONr_scangle_it14.131163060
LS refinement shellResolution: 2.284→2.343 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 154 -
Rwork0.332 2923 -
obs--64.43 %
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)
10.17440.28460.90280.7492.548623.3894-0.0973-0.0704-0.0662-0.02380.1450.00091.1443-0.4489-0.04770.29190.1115-0.02990.3925-0.00770.4624-3.95423.69865.239
20.77970.45622.5156.67091.983320.38940.1894-0.18940.13951.3923-0.6255-0.29420.8301-0.98790.43610.45940.0105-0.12880.43650.00680.28422.6831.72139.85
30.25750.143-0.02920.3132-1.46417.1027-0.2837-0.06540.0629-0.08040.0506-0.1098-0.4160.26670.23320.34580.1016-0.03050.3378-0.03060.45713.44627.6664.951
41.9092-0.8965-3.35194.05412.088544.09210.0381-0.24670.07520.9645-0.16880.21390.7655-1.27720.13080.397-0.0188-0.00970.40420.00620.2821-1.27125.107140.171
50.3269-0.2174-0.23920.31430.828914.492-0.26730.02860.04160.07650.04310.0439-0.7491-0.55450.22420.321-0.04650.03760.2849-0.02930.4523-3.8526.82832.196
60.9194-1.5649-3.99473.05396.044829.38670.30150.4493-0.0189-0.3907-0.90070.04180.3497-2.24260.59910.4004-0.05750.08690.8742-0.14480.22493.96115.978-41.896
70.1811-0.028-0.26840.2373-1.943819.1592-0.2064-0.0064-0.0472-0.0716-0.0238-0.00220.73190.73820.23020.3862-0.0860.02440.3040.01230.4163.91123.52231.95
81.39921.61197.77283.13667.465945.5864-0.0377-0.31950.1205-0.5855-0.54630.2319-0.3569-1.89870.5840.58460.2867-0.03791.436-0.23410.3116-0.77222.072-42.443
90.3344-0.032-1.35010.8451-0.53256.4034-0.04420.0021-0.00950.049-0.17190.06450.2187-0.15520.21610.0398-0.062-0.02220.3039-0.01460.478812.69843.9618.144
103.2340.744-8.211.0279-1.775233.1182-0.691-0.4612-0.15310.70470.001-0.09642.34291.32380.68991.16650.22040.01270.4068-0.02660.19537.51849.2682.612
111.4922-0.1867-4.48220.45261.186718.7626-0.0971-0.0394-0.06060.1309-0.1542-0.06610.94190.36580.25140.22950.0495-0.05090.3174-0.01350.471416.41236.6118.846
121.0793-1.2896-3.50834.81846.312721.4173-0.84510.0378-0.21520.9412-0.26810.78081.2548-0.15341.11320.9986-0.07620.15360.3236-0.09980.37392.15454.20280.467
130.3086-0.06072.28170.58430.109934.80860.06780.1143-0.0919-0.1622-0.1741-0.10470.23890.61330.10630.06340.09880.00530.3814-0.05010.465318.04343.076-23.447
140.73410.17841.61162.07411.883826.3141-0.17720.06980.0885-0.1548-0.11760.05970.0987-0.01410.29480.35920.032-0.05620.31430.01860.26558.18139.357-97.953
150.92390.0344-3.60880.45050.389420.6605-0.10520.0982-0.1896-0.0352-0.25790.1211.1817-0.31170.3630.17890.0006-0.070.3522-0.04090.496814.3135.812-24.153
162.3165-1.84946.24451.529-4.274458.4009-0.24340.36180.0720.1725-0.361-0.1325-0.83691.6480.60440.5377-0.04510.02770.38270.04810.28915.01343.415-98.785
170.09380.13780.39860.5084-0.656415.7032-0.0413-0.0519-0.0473-0.182-0.16810.1106-0.2591-0.78650.20940.10670.1677-0.06080.4576-0.02820.510513.6367.13589.379
183.04613.672811.57336.82817.793850.1824-0.89090.7004-0.0505-0.33610.33710.4757-2.09871.98820.55380.5723-0.23490.03970.6133-0.19650.335710.414-3.56415.322
192.02950.10526.81740.4295-0.148624.1787-0.26480.12190.1261-0.0907-0.1842-0.1055-1.22960.44460.4490.27950.11370.05840.363-0.00590.529717.44514.68988.882
201.39991.44365.22316.664527.8452.8041-0.291-0.0338-0.02420.4507-0.49250.6821-0.001-0.58680.78350.4642-0.22280.15130.4796-0.27020.43873.63-6.09417.885
210.6167-0.04310.1290.44931.10336.06560.04740.02470.10060.0668-0.165-0.0794-0.1253-0.01620.11760.0482-0.07070.01130.29620.00140.471720.4577.184120.887
220.4383-0.7347-1.70883.1310.230152.0741-0.47630.0781-0.08980.6277-0.20360.11741.6235-1.41510.67980.6604-0.15410.10380.4265-0.06040.187214.04310.283195.919
231.5642-0.46615.32180.9083-1.416322.966-0.1543-0.05380.16130.0948-0.34190.212-1.175-0.53770.49610.11150.04510.01720.3612-0.05290.509916.62514.786122.158
242.7281-0.7468-5.00231.75440.905926.5024-1.4326-0.3769-0.39360.5233-0.0961-0.10682.551.18761.52870.81750.14040.1350.39630.08020.275621.0817.341196.445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A51 - 109
2X-RAY DIFFRACTION2A110 - 149
3X-RAY DIFFRACTION3B51 - 109
4X-RAY DIFFRACTION4B110 - 149
5X-RAY DIFFRACTION5C51 - 109
6X-RAY DIFFRACTION6C110 - 149
7X-RAY DIFFRACTION7D51 - 109
8X-RAY DIFFRACTION8D110 - 149
9X-RAY DIFFRACTION9E51 - 109
10X-RAY DIFFRACTION10E110 - 149
11X-RAY DIFFRACTION11F51 - 109
12X-RAY DIFFRACTION12F110 - 149
13X-RAY DIFFRACTION13G51 - 109
14X-RAY DIFFRACTION14G110 - 149
15X-RAY DIFFRACTION15H51 - 109
16X-RAY DIFFRACTION16H110 - 149
17X-RAY DIFFRACTION17I51 - 109
18X-RAY DIFFRACTION18I110 - 149
19X-RAY DIFFRACTION19J51 - 109
20X-RAY DIFFRACTION20J110 - 149
21X-RAY DIFFRACTION21K51 - 109
22X-RAY DIFFRACTION22K110 - 149
23X-RAY DIFFRACTION23L51 - 109
24X-RAY DIFFRACTION24L110 - 149

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