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- PDB-5mue: Self-assembled alpha-Tocopherol Transfer Protein Nanoparticles Pr... -

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Basic information

Entry
Database: PDB / ID: 5mue
TitleSelf-assembled alpha-Tocopherol Transfer Protein Nanoparticles Promote Vitamin E Delivery Across an Endothelial Barrier
ComponentsAlpha-tocopherol transfer protein
KeywordsTRANSPORT PROTEIN / lipid transfer protein / sec14-like
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
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
Similarity search - Domain/homology
ETHANOLAMINE / Chem-VIV / Alpha-tocopherol transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.397 Å
AuthorsStocker, A. / Aeschimann, W.
CitationJournal: Sci Rep / Year: 2017
Title: Self-assembled alpha-Tocopherol Transfer Protein Nanoparticles Promote Vitamin E Delivery Across an Endothelial Barrier.
Authors: Aeschimann, W. / Staats, S. / Kammer, S. / Olieric, N. / Jeckelmann, J.M. / Fotiadis, D. / Netscher, T. / Rimbach, G. / Cascella, M. / Stocker, A.
History
DepositionJan 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Source and taxonomy / Structure summary
Category: entity / entity_src_gen / pdbx_entity_src_syn / Item: _entity.src_method
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Jan 17, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-tocopherol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1935
Polymers26,5701
Non-polymers6234
Water1,17165
1
A: Alpha-tocopherol transfer protein
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)652,630120
Polymers637,67124
Non-polymers14,95996
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area65030 Å2
ΔGint-831 kcal/mol
Surface area224450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.184, 168.184, 168.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-304-

ETA

21A-304-

ETA

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 26569.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTPA, TPP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P49638

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Non-polymers , 5 types, 69 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: 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.: 1 / Source method: obtained synthetically / Formula: C29H50O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ETA / ETHANOLAMINE / Ethanolamine


Type: L-peptide COOH carboxy terminus / Mass: 61.083 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NO
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 7.5
Details: 0.1 M Ammonium sulfate,10% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99987 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 2.397→48.551 Å / Num. obs: 30125 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 10.744 % / Biso Wilson estimate: 51.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rrim(I) all: 0.095 / Χ2: 1.143 / Net I/σ(I): 20.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.5410.6921.5431.5425430.5991.62199.1
2.54-2.7211.0150.9162.824280.8130.96100
2.72-2.9310.4860.5244.922630.940.551100
2.93-3.2111.3890.2629.920900.9850.274100
3.21-3.5911.280.11521.8318950.9970.1299.9
3.59-4.1410.3680.06535.4817010.9990.068100
4.14-5.0610.6940.03856.2614540.9990.0499.9
5.06-7.1210.3590.03953.4211540.9990.04199.7
7.12-48.5519.0970.02371.3170010.02597.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OIP

1oip


Resolution: 2.397→39.641 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 22.76
RfactorNum. reflection% reflection
Rfree0.2152 1503 4.99 %
Rwork0.1823 --
obs0.184 30125 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 165.7 Å2 / Biso mean: 62.3207 Å2 / Biso min: 38.61 Å2
Refinement stepCycle: final / Resolution: 2.397→39.641 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1877 0 41 65 1983
Biso mean--50.37 57.62 -
Num. residues----228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021969
X-RAY DIFFRACTIONf_angle_d0.6172661
X-RAY DIFFRACTIONf_chiral_restr0.025287
X-RAY DIFFRACTIONf_plane_restr0.004330
X-RAY DIFFRACTIONf_dihedral_angle_d12.275718
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3973-2.47460.29091330.30992572270598
2.4746-2.5630.34551350.290526082743100
2.563-2.66560.30741360.276925902726100
2.6656-2.78690.3381380.268326062744100
2.7869-2.93380.29621320.257426032735100
2.9338-3.11760.2881370.230425982735100
3.1176-3.35820.20371420.21126192761100
3.3582-3.69590.21731330.176425832716100
3.6959-4.23020.2181400.161326232763100
4.2302-5.32750.16231370.127826082745100
5.3275-39.64680.15281400.1412612275299
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)
16.5007-4.10743.12918.3692-2.2346.17660.0453-2.0831-1.86170.93181.2196-2.14090.63151.6946-1.16171.0250.039-0.4671.3464-0.01251.500931.395-38.354429.446
25.70540.0413-2.14813.29690.11283.75030.06230.18110.69940.22880.0127-0.3236-0.2613-0.1726-0.04660.6166-0.037-0.12470.5249-0.04730.511423.3763-34.773222.4854
31.88452.9791-3.0034.7526-4.75514.82110.69820.1321-0.1107-0.2088-1.47911.2019-0.5125-0.0370.83691.03570.28230.09431.1-0.18730.631310.6809-38.80333.8287
41.97561.9390.87483.1233-1.39874.910.1804-0.29860.03090.3178-0.34420.05350.2023-0.32370.27640.53010.117-0.04570.74710.10720.377215.4981-56.794935.6005
53.06790.2432-0.23811.8598-0.33342.95870.0833-0.5446-0.17180.27660.04070.0519-0.0682-0.0864-0.15180.41080.1037-0.04970.59030.03960.2913.757-54.386728.7713
67.85821.22396.0936.50011.58524.8145-0.17390.50190.5296-0.27840.064-0.73940.66341.96390.11360.48350.05-0.01360.7696-0.01820.438929.1947-48.058922.2869
73.42841.0172-0.24192.17470.43961.91890.00050.13270.2641-0.07310.04390.3862-0.2273-0.4972-0.03320.39930.1146-0.04490.57930.05870.33256.8093-50.021319.8113
86.58671.5782-1.29356.08140.20226.85470.06710.8737-1.1375-0.7289-0.0521-0.24650.92470.4786-0.06670.56180.1166-0.02860.5426-0.10670.555816.4005-66.009215.0505
94.28370.67722.89932.81053.96096.57240.0142-0.6347-1.15020.4061-0.2928-0.83130.81640.69580.39760.68540.1643-0.00040.68010.24740.623519.7945-65.238330.7961
103.51950.90780.99946.410.72133.9640.0466-0.64580.03970.9746-0.3168-0.5109-0.08640.72950.26160.57580.0085-0.10110.85040.01730.366122.7588-50.508939.5329
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 48:52)A48 - 52
2X-RAY DIFFRACTION2(chain A and resid 53:74)A53 - 74
3X-RAY DIFFRACTION3(chain A and resid 75:85)A75 - 85
4X-RAY DIFFRACTION4(chain A and resid 86:105)A86 - 105
5X-RAY DIFFRACTION5(chain A and resid 106:144)A106 - 144
6X-RAY DIFFRACTION6(chain A and resid 145:153)A145 - 153
7X-RAY DIFFRACTION7(chain A and resid 154:223)A154 - 223
8X-RAY DIFFRACTION8(chain A and resid 224:250)A224 - 250
9X-RAY DIFFRACTION9(chain A and resid 251:259)A251 - 259
10X-RAY DIFFRACTION10(chain A and resid 260:276)A260 - 276

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