[English] 日本語
Yorodumi
- PDB-6zpd: gamma-tocopherol transfer protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zpd
Titlegamma-tocopherol transfer protein
ComponentsAlpha-tocopherol transfer protein
KeywordsLIPID TRANSPORT / SEC-14 like / vitamin E / nanoparticle / transcytosis
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 / phosphatidylinositol bisphosphate binding ...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 / 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
Chem-VIV / Alpha-tocopherol transfer protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsAeschimann, W. / Kammer, S. / Staats, S. / Stocker, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_156419 Switzerland
CitationJournal: Redox Biol / Year: 2020
Title: Engineering of a functional gamma-tocopherol transfer protein.
Authors: Aeschimann, W. / Kammer, S. / Staats, S. / Schneider, P. / Schneider, G. / Rimbach, G. / Cascella, M. / Stocker, A.
History
DepositionJul 8, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-tocopherol transfer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6606
Polymers26,9401
Non-polymers7205
Water3,063170
1
A: Alpha-tocopherol transfer protein
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)663,837144
Polymers646,56124
Non-polymers17,276120
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 area82890 Å2
ΔGint-1060 kcal/mol
Surface area218360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.687, 167.687, 167.687
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-

TRS

21A-305-

TRS

31A-527-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

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


Mass: 26940.059 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 (E. coli) / References: UniProt: P49638

-
Non-polymers , 5 types, 175 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 / Feature type: SUBJECT OF INVESTIGATION
#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-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.65 Å3/Da / Density % sol: 66.27 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 4000, ammonium sulfate, HEPES

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0007 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0007 Å / Relative weight: 1
ReflectionResolution: 2.24→48.407 Å / Num. obs: 19658 / % possible obs: 99.8 % / Redundancy: 10.87 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 21.8
Reflection shellResolution: 2.24→2.38 Å / Redundancy: 10.92 % / Rmerge(I) obs: 0.686 / Num. unique obs: 3107 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OIP

1oip


Resolution: 2.24→48.407 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.85 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2178 982 5 %
Rwork0.182 18675 -
obs0.1837 19657 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.84 Å2 / Biso mean: 45.953 Å2 / Biso min: 19.58 Å2
Refinement stepCycle: final / Resolution: 2.24→48.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1904 0 41 170 2115
Biso mean--44.69 53.35 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022028
X-RAY DIFFRACTIONf_angle_d0.6322742
X-RAY DIFFRACTIONf_chiral_restr0.026295
X-RAY DIFFRACTIONf_plane_restr0.003343
X-RAY DIFFRACTIONf_dihedral_angle_d12.427752
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.24-2.35770.26651370.235260899
2.3577-2.50540.25661380.22392626100
2.5054-2.69880.25151380.20472612100
2.6988-2.97040.22741390.20272640100
2.9704-3.40010.24571390.18272658100
3.4001-4.28340.18421420.16642694100
4.2834-6.660.20271490.16412837100
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)
10.2635-0.0028-0.17840.49710.17070.1398-0.0052-0.29520.53980.27210.0301-0.31-0.4460.26890.00010.39640.0086-0.07930.3696-0.0370.409523.7191-34.808524.0831
20.03880.0401-0.01350.0444-0.03240.02320.6013-0.0602-0.33490.23490.67980.0692-0.5118-0.36180.0020.63980.14990.19520.723-0.08140.73457.72-37.631732.9196
30.6660.70370.18431.0078-0.37610.7496-0.0389-0.0610.01720.0930.0632-0.00990.0913-0.086200.22650.0912-0.01970.35040.01270.180617.0364-56.239829.8228
40.4565-0.42480.63130.9092-0.09180.9511-0.1806-0.16220.06330.0940.1170.0667-0.0475-0.002-00.24310.0456-0.00740.3716-0.00110.164815.3734-51.277229.0111
50.66430.27880.087-0.04680.45571.281-0.050.04160.0691-0.12480.03390.2265-0.1046-0.2927-00.21140.0548-0.03180.38530.03880.26596.1045-50.954922.4329
60.12780.1371-0.09030.2052-0.00960.0131-0.46430.29040.6383-0.73680.32990.4971-0.1961-0.5171-0.00070.36790.095-0.11060.53920.08370.43841.8251-45.702616.8267
70.7025-0.0057-0.16190.47380.4220.4498-0.05711.00430.3402-0.1539-0.26170.0435-0.0962-0.6901-0.19620.38490.0448-0.11670.57920.13830.279611.8785-46.786510.8905
80.01890.0640.09280.4010.16080.4919-0.06570.4946-0.4032-0.3515-0.0149-0.07550.71830.0876-0.00270.39730.0617-0.00810.4101-0.05050.322516.4232-65.888114.8498
90.4680.47120.40070.86670.73880.6912-0.1078-0.7188-0.0906-0.3261-0.2314-0.15490.40340.2493-0.09410.4560.2109-0.02720.3680.20440.319119.4453-66.287730.5979
100.2513-0.00950.00240.4469-0.08890.44630.0896-0.29780.2951-0.2215-0.1375-0.6018-0.29680.13450.01280.39510.0871-0.07180.47760.05220.233522.4799-48.910838.7856
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 48:75)A48 - 75
2X-RAY DIFFRACTION2(chain A and resid 76:83)A76 - 83
3X-RAY DIFFRACTION3(chain A and resid 84:120)A84 - 120
4X-RAY DIFFRACTION4(chain A and resid 121:158)A121 - 158
5X-RAY DIFFRACTION5(chain A and resid 159:203)A159 - 203
6X-RAY DIFFRACTION6(chain A and resid 204:215)A204 - 215
7X-RAY DIFFRACTION7(chain A and resid 216:223)A216 - 223
8X-RAY DIFFRACTION8(chain A and resid 224:250)A224 - 250
9X-RAY DIFFRACTION9(chain A and resid 251:258)A251 - 258
10X-RAY DIFFRACTION10(chain A and resid 259:278)A259 - 278

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more