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- PDB-3w67: Crystal structure of mouse alpha-tocopherol transfer protein in c... -

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Basic information

Entry
Database: PDB / ID: 3w67
TitleCrystal structure of mouse alpha-tocopherol transfer protein in complex with alpha-tocopherol and phosphatidylinositol-(3,4)-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 / vitamin E binding / intracellular pH reduction / vitamin E metabolic process / lipid transfer activity / vitamin binding / vitamin transport / negative regulation of establishment of blood-brain barrier / intermembrane lipid transfer / positive regulation of amyloid-beta clearance ...Vitamin E / vitamin E binding / intracellular pH reduction / vitamin E metabolic process / lipid transfer activity / vitamin binding / vitamin transport / negative regulation of establishment of blood-brain barrier / intermembrane lipid transfer / positive regulation of amyloid-beta clearance / negative regulation of epithelial cell apoptotic process / phosphatidylinositol-3,4-bisphosphate binding / response to pH / phosphatidylinositol bisphosphate binding / embryonic placenta development / phosphatidylinositol-4,5-bisphosphate binding / placenta development / response to toxic substance / late endosome / 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-3PT / Chem-VIV / Alpha-tocopherol transfer protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.61 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 1.2Nov 8, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)126,75712
Polymers122,4974
Non-polymers4,2608
Water1,53185
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)31,6893
Polymers30,6241
Non-polymers1,0652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Alpha-tocopherol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6893
Polymers30,6241
Non-polymers1,0652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Alpha-tocopherol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6893
Polymers30,6241
Non-polymers1,0652
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Alpha-tocopherol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6893
Polymers30,6241
Non-polymers1,0652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.285, 69.665, 87.183
Angle α, β, γ (deg.)100.24, 109.72, 100.46
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 430.706 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H50O2
#3: Chemical
ChemComp-3PT / (2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate


Mass: 634.354 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H33O19P3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
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: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 35518 / Rsym value: 0.077

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R5L

1r5l


Resolution: 2.61→28.41 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.915 / SU B: 28.499 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2595 1774 5 %RANDOM
Rwork0.21078 ---
obs0.2133 33738 95.51 %-
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: 78.311 Å2
Baniso -1Baniso -2Baniso -3
1-0.21 Å2-0.14 Å20.17 Å2
2---0.37 Å20.1 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.61→28.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8203 0 280 85 8568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228695
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.99511797
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.25251001
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.33922.682399
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.845151474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3891576
X-RAY DIFFRACTIONr_chiral_restr0.0920.21303
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_it0.8381.55025
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51828148
X-RAY DIFFRACTIONr_scbond_it1.7533670
X-RAY DIFFRACTIONr_scangle_it2.734.53649
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.61→2.679 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.424 94 -
Rwork0.39 2083 -
obs--79.37 %
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)
17.1618-0.00373.06713.06931.57046.2249-1.0823-0.59140.36290.31790.3597-0.0837-1.0245-0.03730.72250.56080.1791-0.24830.3229-0.05910.13625.7654.72718.523
22.50630.45410.79242.6732-0.05392.5426-0.32270.24380.10550.03940.1136-0.0087-0.27430.12520.20910.09960.029-0.02140.28330.010.0645-0.295-2.222-4.245
32.7089-0.9086-0.78634.61881.59637.4722-0.0641-0.98340.12640.6067-0.22220.49930.3622-0.37040.28630.2311-0.07840.14380.5493-0.07090.156225.196-19.05929.33
42.80740.3631-0.48272.59850.44463.01610.1807-0.1111-0.3293-0.0306-0.08230.06230.54930.0175-0.09840.15470.0417-0.02960.1822-0.00030.206929.794-28.8946.732
57.0574-3.3671.40826.4366-2.59317.6113-0.07451.21830.0147-0.7818-0.5057-0.7964-0.55790.7840.58020.2585-0.1020.11320.50860.02510.18713.315-44.321-45.374
62.7524-0.510.09113.6189-0.22285.1027-0.10380.0015-0.01530.2349-0.06840.2027-0.8054-0.22250.17220.22070.0158-0.02280.1657-0.03970.0840.95-41.191-26.065
76.31022.75391.100312.82387.414612.1640.69950.0733-0.30620.2532-0.0927-0.26740.6236-0.0298-0.60680.2453-0.08440.0070.6620.19510.257927.262-13.448-44.295
89.46160.46881.078617.61017.94897.76731.5478-0.3495-0.94673.61720.2563-1.45042.62661.0709-1.80411.2279-0.0177-0.70771.0265-0.0350.516132.058-13.434-32.12
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 73
2X-RAY DIFFRACTION2A74 - 275
3X-RAY DIFFRACTION3B23 - 67
4X-RAY DIFFRACTION4B68 - 275
5X-RAY DIFFRACTION5C26 - 87
6X-RAY DIFFRACTION6C88 - 275
7X-RAY DIFFRACTION7D25 - 163
8X-RAY DIFFRACTION8D164 - 275

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