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- PDB-1oiz: The Molecular Basis of Vitamin E Retention: Structure of Human Al... -

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Basic information

Entry
Database: PDB / ID: 1oiz
TitleThe Molecular Basis of Vitamin E Retention: Structure of Human Alpha-Tocopherol Transfer Protein
ComponentsALPHA-TOCOPHEROL TRANSFER PROTEIN
KeywordsTRANSPORT / ATAXIA / AVED / TRANSFER PROTEIN / TOCOPHEROL / VITAMIN E
Function / homology
Function and homology information


Vitamin E / vitamin E binding / vitamin E metabolic process / lipid transfer activity / vitamin transport / negative regulation of establishment of blood-brain barrier / intermembrane lipid transfer / positive regulation of amyloid-beta clearance / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol bisphosphate binding ...Vitamin E / vitamin E binding / vitamin E metabolic process / lipid transfer activity / vitamin transport / negative regulation of establishment of blood-brain barrier / intermembrane lipid transfer / positive regulation of amyloid-beta clearance / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol bisphosphate binding / embryonic placenta development / phosphatidylinositol-4,5-bisphosphate binding / lipid metabolic process / response to toxic substance / late endosome / cytosol
Similarity search - Function
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) ...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 / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Alpha-tocopherol transfer protein
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.88 Å
AuthorsMeier, R. / Tomizaki, T. / Schulze-Briese, C. / Baumann, U. / Stocker, A.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: The Molecular Basis of Vitamin E Retention: Structure of Human Alpha-Tocopherol Transfer Protein
Authors: Meier, R. / Tomizaki, T. / Schulze-Briese, C. / Baumann, U. / Stocker, A.
History
DepositionJun 27, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6988
Polymers63,5832
Non-polymers2,1156
Water5,296294
1
A: ALPHA-TOCOPHEROL TRANSFER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8494
Polymers31,7921
Non-polymers1,0583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ALPHA-TOCOPHEROL TRANSFER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8494
Polymers31,7921
Non-polymers1,0583
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.144, 113.775, 67.433
Angle α, β, γ (deg.)90.00, 98.95, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A15 - 270
2114B15 - 270
DetailsTHE TWO MOLECULES IN THIS STRUCTURE HAVE TRT MOLECULESAT THE INTERFACE AND HAVE A BURIED SURFACE AREA OFOF 961.2 ANGSTROM**2

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Components

#1: Protein ALPHA-TOCOPHEROL TRANSFER PROTEIN / ALPHA-TTP / TTPA / TPP1


Mass: 31791.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CONTAINS CRAL_TRIO LIPID BINDING DOMAIN, RESIDUES 89-275
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P49638
#2: Chemical
ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE / Triton X-100


Mass: 352.508 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: BINDS ALPHA-TOCOPHEROL AND ENHANCES ITS TRANSFER BETWEEN SEPARATE MEMBRANES. DISEASE: ...FUNCTION: BINDS ALPHA-TOCOPHEROL AND ENHANCES ITS TRANSFER BETWEEN SEPARATE MEMBRANES. DISEASE: DEFECTS IN TTPA ARE THE CAUSE OF ATAXIA WITH ISOLATED VITAMIN E DEFICIENCY

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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: 2.69 Å3/Da / Density % sol: 54.28 %
Crystal growpH: 7.5 / Details: 5% PEG 6000, 0.1 M HEPES PH 7.5, 15% (V/V) MPD
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 mg/mlprotein1drop
25 %(w/v)PEG60001reservoir
30.1 MHEPES1reservoirpH7.5
415 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9791
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 54206 / % possible obs: 99.3 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.2
Reflection shellResolution: 1.88→1.9 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.2 / % possible all: 93.1
Reflection
*PLUS
Highest resolution: 1.88 Å / Lowest resolution: 30 Å / Num. measured all: 345927 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 93.1 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.88→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.367 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2711 5 %RANDOM
Rwork0.195 ---
obs0.197 51495 99.4 %-
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: 25.73 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å2-1.21 Å2
2---0.95 Å20 Å2
3---2.21 Å2
Refinement stepCycle: LAST / Resolution: 1.88→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 0 150 294 4733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214557
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.9886177
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6055527
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0840.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023396
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.22298
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2305
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.254
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1250.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5341.52653
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00224299
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.59831904
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6214.51878
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.93 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 194
Rwork0.256 3689
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)
11.6550.46270.0892.804-0.10461.03240.0344-0.19640.03160.30120.00950.09230.1174-0.0616-0.04390.1313-0.01940.02180.12230.02450.0140.7678.20551.615
22.0282-0.19860.332.4580.35370.9050.00410.2584-0.0196-0.2459-0.04450.0045-0.20170.07230.04040.12350.0070.03290.0988-0.02150.025622.428-5.59121.156
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 273
2X-RAY DIFFRACTION2B11 - 274
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3

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