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

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Basic information

Entry
Database: PDB / ID: 5mug
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 / intermembrane lipid transfer / negative regulation of establishment of blood-brain barrier / 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 / intermembrane lipid transfer / negative regulation of establishment of blood-brain barrier / 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: 2.42 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
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-tocopherol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5576
Polymers26,8981
Non-polymers6595
Water1,00956
1
A: Alpha-tocopherol transfer protein
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)661,362144
Polymers645,55124
Non-polymers15,810120
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 area73800 Å2
ΔGint-1081 kcal/mol
Surface area227360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.259, 168.259, 168.259
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-305-

ETA

21A-305-

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: 26897.979 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, 61 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.: 1 / Source method: obtained synthetically / Formula: C29H50O2
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ETA / 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


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.69 Å3/Da / Density % sol: 66.66 %
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: 1.0079 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0079 Å / Relative weight: 1
ReflectionResolution: 2.42→48.572 Å / Num. obs: 29032 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.813 % / Biso Wilson estimate: 60.22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.096 / Χ2: 1.114 / Net I/σ(I): 14 / Num. measured all: 139722
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.42-2.574.7721.1951.4145760.5291.34395.9
2.57-2.744.7460.762.2944450.6870.85799.8
2.74-2.964.7560.463.9541320.8670.51899
2.96-3.245.0660.247.7138150.9710.26899.8
3.24-3.624.650.1114.8133990.9910.12498.9
3.62-4.184.9050.0624.530410.9970.06799.3
4.18-5.114.8440.03836.6525370.9980.04298.4
5.11-7.194.7710.03736.2419780.9980.04198.6
7.19-48.5724.8350.02449.3911090.9990.02797

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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: 2.42→48.572 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 23.27
RfactorNum. reflection% reflection
Rfree0.2117 787 5 %
Rwork0.1906 --
obs0.1916 15732 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.69 Å2 / Biso mean: 67.8465 Å2 / Biso min: 38.33 Å2
Refinement stepCycle: final / Resolution: 2.42→48.572 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1901 0 42 56 1999
Biso mean--54.69 61.73 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032025
X-RAY DIFFRACTIONf_angle_d0.682740
X-RAY DIFFRACTIONf_chiral_restr0.027295
X-RAY DIFFRACTIONf_plane_restr0.004343
X-RAY DIFFRACTIONf_dihedral_angle_d13.144744
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4191-2.57060.38261250.35182380250597
2.5706-2.76910.30051290.286824542583100
2.7691-3.04770.26221300.265824682598100
3.0477-3.48860.2341310.21424892620100
3.4886-4.39480.20261330.165225162649100
4.3948-48.5820.16481390.14972638277799
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)
18.6299-4.75317.37862.8348-4.49278.21810.0119-1.0746-0.06342.06680.0295-2.35770.61790.98180.02821.36360.2389-0.26261.7568-0.09351.382531.5828-37.748429.9894
22.77262.3201-3.99138.3919-4.3786.65520.19510.3080.49220.55170.10430.5479-0.9098-0.455-0.20370.76240.0455-0.08670.6975-0.05750.718418.7285-35.62425.8888
33.73794.35910.04825.3886-1.04164.00840.1261-0.6851-0.06860.6358-0.29990.28660.444-0.10840.18310.48520.0508-0.06050.72480.01790.427315.5591-56.601935.6344
43.0764-0.05560.45763.0688-0.32314.9536-0.0967-0.1176-0.10460.13640.0401-0.02680.1218-0.09650.03470.41630.0509-0.04930.55830.03880.358914.9626-53.901726.718
54.52170.7872-0.26162.81610.32681.9404-0.08510.04230.6128-0.04590.0140.5599-0.2493-0.50690.07040.46470.0643-0.07210.64750.06230.46976.7755-49.248322.3607
67.89356.1188-4.24064.8878-4.27849.0806-0.60150.23940.2603-0.90630.09780.3941-0.4025-0.51340.5370.60180.1125-0.06611.04980.10420.79021.9466-45.866616.9159
73.4724-0.7201-0.3836.6948-1.57172.8045-0.06860.63080.0935-1.57550.03440.24080.0242-0.59430.0090.65830.0039-0.06180.89270.10420.404910.2264-53.054511.767
87.64361.56640.50387.6447-0.9365.74050.22980.789-1.007-0.4841-0.4967-0.43470.82580.60090.06610.70030.13570.07580.7053-0.07640.604218.6385-66.731716.3411
94.09546.22653.93669.46995.97833.79540.06590.0278-0.85030.5188-0.4942-0.94720.68370.48650.33260.83690.13740.00350.81690.130.659520.3909-64.413931.7626
104.1405-0.43950.02632.05463.28536.9095-0.2137-0.62980.26820.96010.1529-0.4184-0.58120.42260.12720.87470.096-0.13590.77030.02640.57222.502-48.332339.4797
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 53:85)A53 - 85
3X-RAY DIFFRACTION3(chain A and resid 86:105)A86 - 105
4X-RAY DIFFRACTION4(chain A and resid 106:164)A106 - 164
5X-RAY DIFFRACTION5(chain A and resid 165:203)A165 - 203
6X-RAY DIFFRACTION6(chain A and resid 204:215)A204 - 215
7X-RAY DIFFRACTION7(chain A and resid 216:229)A216 - 229
8X-RAY DIFFRACTION8(chain A and resid 230:252)A230 - 252
9X-RAY DIFFRACTION9(chain A and resid 253:259)A253 - 259
10X-RAY DIFFRACTION10(chain A and resid 260:278)A260 - 278

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