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- PDB-3w68: Crystal structure of mouse alpha-tocopherol transfer protein in c... -

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Basic information

Entry
Database: PDB / ID: 3w68
TitleCrystal structure of mouse alpha-tocopherol transfer protein in complex with alpha-tocopherol and phosphatidylinositol-(4,5)-bisphosphate
ComponentsAlpha-tocopherol transfer protein
KeywordsTRANSPORT PROTEIN / Ataxia / Vitamin E deficiency / AVED / Transfer protein / Tocopherol / Vitamin E / Disease mutation / alpha-tocopherol transfer / alpha-tocopherol / phosphatidyl inositol phosphates
Function / homology
Function and homology information


Vitamin E transport / vitamin E binding / vitamin E metabolic process / lipid transfer activity / vitamin transport / intermembrane lipid transfer / negative regulation of establishment of blood-brain barrier / positive regulation of amyloid-beta clearance / phosphatidylinositol-3,4-bisphosphate binding / embryonic placenta development ...Vitamin E transport / vitamin E binding / vitamin E metabolic process / lipid transfer activity / vitamin transport / intermembrane lipid transfer / negative regulation of establishment of blood-brain barrier / positive regulation of amyloid-beta clearance / phosphatidylinositol-3,4-bisphosphate binding / embryonic placenta development / phosphatidylinositol-4,5-bisphosphate binding / placenta development / response to toxic substance / cytoplasm
Similarity search - Function
Alpha-tocopherol transfer / N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. ...Alpha-tocopherol transfer / N-terminal domain of phosphatidylinositol transfer protein sec14p / Phosphatidylinositol Transfer Protein Sec14p / CRAL-TRIO lipid binding domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain / CRAL/TRIO, N-terminal domain superfamily / CRAL/TRIO domain / CRAL-TRIO lipid binding domain profile. / Domain in homologues of a S. cerevisiae phosphatidylinositol transfer protein (Sec14p) / CRAL-TRIO lipid binding domain / CRAL-TRIO lipid binding domain superfamily / Helicase, Ruva Protein; domain 3 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4PT / Chem-PBU / PHOSPHATE ION / Chem-VIV / Alpha-tocopherol transfer protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsOhto, U. / Satow, Y.
CitationJournal: Science / Year: 2013
Title: Impaired alpha-TTP-PIPs interaction underlies familial vitamin E deficiency
Authors: Kono, N. / Ohto, U. / Hiramatsu, T. / Urabe, M. / Uchida, Y. / Satow, Y. / Arai, H.
History
DepositionFeb 11, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Jan 29, 2014Group: Non-polymer description
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _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: Alpha-tocopherol transfer protein
B: Alpha-tocopherol transfer protein
C: Alpha-tocopherol transfer protein
D: Alpha-tocopherol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,38316
Polymers122,4974
Non-polymers4,88612
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Alpha-tocopherol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4884
Polymers30,6241
Non-polymers1,8633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Alpha-tocopherol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4064
Polymers30,6241
Non-polymers1,7813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Alpha-tocopherol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3405
Polymers30,6241
Non-polymers7164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Alpha-tocopherol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1503
Polymers30,6241
Non-polymers5262
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.977, 69.620, 87.097
Angle α, β, γ (deg.)100.88, 109.45, 100.01
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Alpha-tocopherol transfer protein / Alpha-TTP


Mass: 30624.289 Da / Num. of mol.: 4 / Fragment: UNP residues 21-275
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ttpa / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8BWP5

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Non-polymers , 5 types, 259 molecules

#2: Chemical
ChemComp-VIV / (2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL


Mass: 430.706 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H50O2
#3: Chemical ChemComp-4PT / (2R)-3-{[(S)-{[(2S,3R,5S,6S)-2,6-DIHYDROXY-3,4,5-TRIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-(1-HYDROXY BUTOXY)PROPYL BUTYRATE / DIC4-PHOSPHATIDYLINOSITOL(3,4,5)TRISPHOSPHATE


Mass: 716.350 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H36O22P4
#4: Chemical ChemComp-PBU / (2R)-3-{[(R)-HYDROXY{[(1R,2R,3S,4R,5R,6S)-2,3,6-TRIHYDROXY-4,5-BIS(PHOSPHONOOXY)CYCLOHEXYL]OXY}PHOSPHORYL]OXY}PROPANE-1 ,2-DIYL DIBUTANOATE / di-butanoyl L-alpha-phosphatidyl-D-myo-inositol 4,5-bisphosphate / di-C4-PIP2


Mass: 634.354 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H33O19P3
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.57 Å3/Da / Density % sol: 52.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 4-7%(w/v) PEG3350, 15%(w/v) MPD, 85mM NaCl, 85mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 75088 / Rsym value: 0.065

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R5L

1r5l


Resolution: 2.05→29.32 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.132 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23128 3771 5 %RANDOM
Rwork0.19888 ---
obs0.20055 71243 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 75.365 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å2-0.19 Å2-0.32 Å2
2--0.15 Å2-0.06 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8230 0 255 247 8732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0228694
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9911802
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.21351003
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45622.682399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.629151489
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3681576
X-RAY DIFFRACTIONr_chiral_restr0.0940.21301
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216448
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.771.55036
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.42728171
X-RAY DIFFRACTIONr_scbond_it1.97633658
X-RAY DIFFRACTIONr_scangle_it3.1914.53631
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.099 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 262 -
Rwork0.267 5172 -
obs--96.74 %
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)
12.6690.79231.40061.6820.49035.3193-0.7072-0.34210.16920.4101-0.0294-0.2779-0.57630.16730.73660.46450.0907-0.21770.1848-0.00590.18527.6664.32915.747
21.3518-0.10640.24451.7602-0.34991.2081-0.17770.14760.04360.12450.0111-0.0518-0.0978-0.02150.16660.09130.0091-0.04060.2029-0.00790.054-1.174-2.402-4.873
30.77940.32591.71444.63272.47315.10540.205-0.35920.0480.7033-0.32330.47140.5469-0.55960.11830.246-0.17320.13320.317-0.10150.097522.704-21.56225.54
41.65080.7021-0.04871.63110.31252.45920.1004-0.0428-0.13630.1188-0.0677-0.01070.52640.0528-0.03270.21180.0227-0.04220.056-0.01420.111831.189-29.2085.283
58.2675.14214.10273.28573.968335.61971.14230.0085-2.650.45-0.0619-1.7598-1.01240.7292-1.08041.97480.02290.55521.43280.31711.404314.641-43.592-55.295
61.1450.0317-0.44041.6319-0.09943.2084-0.19250.1011-0.0930.01630.0230.0985-0.4256-0.13860.16950.2167-0.0234-0.06980.11730.00160.062.94-41.576-29.69
76.05830.198211.06830.01410.384320.7324-0.03330.96740.5162-0.0258-0.14-0.08870.70361.02050.17341.1585-0.568-0.02791.8140.32151.722321.249-21.067-59.809
83.2975-0.9109-0.16811.99620.07645.03050.52410.63210.3136-0.31460.0101-0.02560.24650.1676-0.53430.1793-0.0422-0.01460.4290.10760.099728.877-12.517-36.286
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 83
2X-RAY DIFFRACTION2A84 - 275
3X-RAY DIFFRACTION3B23 - 87
4X-RAY DIFFRACTION4B88 - 275
5X-RAY DIFFRACTION5C26 - 38
6X-RAY DIFFRACTION6C39 - 277
7X-RAY DIFFRACTION7D25 - 46
8X-RAY DIFFRACTION8D47 - 275

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