[English] 日本語
Yorodumi
- PDB-5i9j: Structure of the cholesterol and lutein-binding domain of human S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5i9j
TitleStructure of the cholesterol and lutein-binding domain of human STARD3 at 1.74A
ComponentsStAR-related lipid transfer protein 3
KeywordsTRANSPORT PROTEIN / lutein-binding protein / helix-grip fold / START / non-vesicular lipid transport
Function / homology
Function and homology information


vesicle tethering to endoplasmic reticulum / progesterone biosynthetic process / endoplasmic reticulum-endosome membrane contact site / organelle membrane contact site / Pregnenolone biosynthesis / cholesterol transfer activity / cholesterol transport / cholesterol binding / mitochondrial transport / steroid metabolic process ...vesicle tethering to endoplasmic reticulum / progesterone biosynthetic process / endoplasmic reticulum-endosome membrane contact site / organelle membrane contact site / Pregnenolone biosynthesis / cholesterol transfer activity / cholesterol transport / cholesterol binding / mitochondrial transport / steroid metabolic process / cholesterol metabolic process / lipid metabolic process / late endosome membrane / endosome / lysosomal membrane / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / protein homodimerization activity / mitochondrion / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
MENTAL domain / StAR-related lipid transfer protein 3, C-terminal / Cholesterol-capturing domain / MENTAL domain profile. / Steroidogenic acute regulatory protein-like / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain ...MENTAL domain / StAR-related lipid transfer protein 3, C-terminal / Cholesterol-capturing domain / MENTAL domain profile. / Steroidogenic acute regulatory protein-like / in StAR and phosphatidylcholine transfer protein / START domain / START domain / START domain profile. / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / StAR-related lipid transfer protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsHorvath, M.P. / Bernstein, P.S. / Li, B. / George, E.W. / Tran, Q.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Eye Institute (NIH/NEI)EY11600 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Structure of the lutein-binding domain of human StARD3 at 1.74 angstrom resolution and model of a complex with lutein.
Authors: Horvath, M.P. / George, E.W. / Tran, Q.T. / Baumgardner, K. / Zharov, G. / Lee, S. / Sharifzadeh, H. / Shihab, S. / Mattinson, T. / Li, B. / Bernstein, P.S.
History
DepositionFeb 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 2023Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: StAR-related lipid transfer protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4216
Polymers25,9881
Non-polymers4325
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.390, 83.390, 82.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-785-

HOH

21A-810-

HOH

-
Components

#1: Protein StAR-related lipid transfer protein 3 / Metastatic lymph node gene 64 protein / MLN 64 / Protein CAB1 / START domain-containing protein 3 / StARD3


Mass: 25988.434 Da / Num. of mol.: 1 / Fragment: lutein-binding domain (UNP residues 216-444)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: STARD3, CAB1, MLN64 / Plasmid: pET22b(+)
Details (production host): F- ompT hsdSB(rB- mB-) gal dcm lacY1 ahpC (DE3) gor522:: Tn10 trxB (KanR, TetR)
Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Origami B / References: UniProt: Q14849
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 61 % / Description: hexagonal rod
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: 0.85 M sodium/potassium tartrate, 0.2 M lithium sulfate, 0.1 M CHES, 0.01 M dithiothreitol. Cryostabilizer: 18% ethylene glycol, 5% ethanol in addition to 0.8M sodium/potassium tartrate, 0.1 ...Details: 0.85 M sodium/potassium tartrate, 0.2 M lithium sulfate, 0.1 M CHES, 0.01 M dithiothreitol. Cryostabilizer: 18% ethylene glycol, 5% ethanol in addition to 0.8M sodium/potassium tartrate, 0.1 M CHES pH 9.1, 0.2 M lithium sulfate, 0.01 M dithiothreitol. Crystals were frozen in propane and stored under liquid nitrogen
Temp details: ambient

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.11583 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2015
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11583 Å / Relative weight: 1
ReflectionResolution: 1.74→37.18 Å / Num. obs: 34160 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.046 / Net I/σ(I): 25.8
Reflection shellResolution: 1.74→1.79 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.4 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIXdev-2276refinement
XDSdata reduction
XSCALEdata scaling
Coot0.8.2 (CCP4)model building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1em2

1em2


Resolution: 1.74→37.18 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 19.19
Details: riding hydrogens, 17 residues with alternate conformations,
RfactorNum. reflection% reflection
Rfree0.1919 1712 5.01 %
Rwork0.1688 --
obs0.17 34159 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.5 Å2
Refinement stepCycle: LAST / Resolution: 1.74→37.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1695 0 27 215 1937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131873
X-RAY DIFFRACTIONf_angle_d1.1612549
X-RAY DIFFRACTIONf_dihedral_angle_d14.261123
X-RAY DIFFRACTIONf_chiral_restr0.071279
X-RAY DIFFRACTIONf_plane_restr0.01333
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7401-1.79130.321410.25262624X-RAY DIFFRACTION99
1.7913-1.84910.24481400.22252656X-RAY DIFFRACTION99
1.8491-1.91520.24071450.20692648X-RAY DIFFRACTION99
1.9152-1.99190.2241350.19182688X-RAY DIFFRACTION99
1.9919-2.08250.20441420.1792675X-RAY DIFFRACTION100
2.0825-2.19230.20681460.17662681X-RAY DIFFRACTION100
2.1923-2.32970.22381430.16732704X-RAY DIFFRACTION100
2.3297-2.50950.20421380.1652689X-RAY DIFFRACTION100
2.5095-2.7620.17311420.16652707X-RAY DIFFRACTION100
2.762-3.16140.17131440.16372743X-RAY DIFFRACTION100
3.1614-3.98230.18981470.15222754X-RAY DIFFRACTION100
3.9823-37.19240.16711490.16272878X-RAY DIFFRACTION100

+
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