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- PDB-4ph7: Structure of Osh6p in complex with phosphatidylinositol 4-phosphate -

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Basic information

Entry
Database: PDB / ID: 4ph7
TitleStructure of Osh6p in complex with phosphatidylinositol 4-phosphate
ComponentsOxysterol-binding protein homolog 6
KeywordsLIPID TRANSPORT / Transport Protein / Osh proteins Phosphatidylinositol Phosphate Lipid transport
Function / homology
Function and homology information


Synthesis of bile acids and bile salts / Acyl chain remodelling of PS / sterol transfer activity / : / sterol transport / sterol homeostasis / phospholipid transporter activity / sterol binding / cortical endoplasmic reticulum / phosphatidylinositol-5-phosphate binding ...Synthesis of bile acids and bile salts / Acyl chain remodelling of PS / sterol transfer activity / : / sterol transport / sterol homeostasis / phospholipid transporter activity / sterol binding / cortical endoplasmic reticulum / phosphatidylinositol-5-phosphate binding / sterol metabolic process / maintenance of cell polarity / piecemeal microautophagy of the nucleus / phosphatidic acid binding / phospholipid transport / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-4-phosphate binding / phosphatidylinositol-3,5-bisphosphate binding / phosphatidylserine binding / exocytosis / endocytosis / intracellular membrane-bounded organelle / lipid binding / endoplasmic reticulum membrane / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature.
Similarity search - Domain/homology
Chem-2Y5 / Oxysterol-binding protein homolog 6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsDelfosse, V. / Moser von Filseck, J. / Antonny, B. / Bourguet, W. / Drin, G.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research Agency2010-1503-01 France
ERC programAdvanced Grant 268888
CitationJournal: Science / Year: 2015
Title: INTRACELLULAR TRANSPORT. Phosphatidylserine transport by ORP/Osh proteins is driven by phosphatidylinositol 4-phosphate.
Authors: Moser von Filseck, J. / Copic, A. / Delfosse, V. / Vanni, S. / Jackson, C.L. / Bourguet, W. / Drin, G.
History
DepositionMay 5, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Dec 27, 2017Group: Structure summary / Category: struct_keywords / Item: _struct_keywords.text
Revision 2.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxysterol-binding protein homolog 6
B: Oxysterol-binding protein homolog 6
C: Oxysterol-binding protein homolog 6
D: Oxysterol-binding protein homolog 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,1058
Polymers207,2364
Non-polymers3,8684
Water9,782543
1
A: Oxysterol-binding protein homolog 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7762
Polymers51,8091
Non-polymers9671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxysterol-binding protein homolog 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7762
Polymers51,8091
Non-polymers9671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Oxysterol-binding protein homolog 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7762
Polymers51,8091
Non-polymers9671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Oxysterol-binding protein homolog 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7762
Polymers51,8091
Non-polymers9671
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.110, 122.260, 141.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Oxysterol-binding protein homolog 6


Mass: 51809.020 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: OSH6, YKR003W, YK102 / Plasmid: pGEX-4T-3 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02201
#2: Chemical
ChemComp-2Y5 / (2R)-1-{[(R)-hydroxy{[(1R,2R,3R,4R,5S,6R)-2,3,5,6-tetrahydroxy-4-(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy)propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate / Phosphatidylinositol-4-phosphate / PI4P


Mass: 967.108 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C47H84O16P2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 543 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.98 % / Description: Needles Urchins
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.5
Details: 200 mM Ammonium Acetate, 100 mM BisTris, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97298 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97298 Å / Relative weight: 1
ReflectionResolution: 2.55→48.56 Å / Num. obs: 77182 / % possible obs: 100 % / Redundancy: 8.2 % / Biso Wilson estimate: 36.8 Å2 / Rsym value: 0.106 / Net I/σ(I): 15.65
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 4.95 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphenix.mrphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4B2Z
Resolution: 2.55→48.562 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 23.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 3257 5 %Random
Rwork0.188 ---
obs0.1905 65141 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→48.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12690 0 260 543 13493
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313294
X-RAY DIFFRACTIONf_angle_d0.72718029
X-RAY DIFFRACTIONf_dihedral_angle_d14.0135185
X-RAY DIFFRACTIONf_chiral_restr0.0361946
X-RAY DIFFRACTIONf_plane_restr0.0042323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.58810.36961420.31012679X-RAY DIFFRACTION100
2.5881-2.62850.39651370.26522624X-RAY DIFFRACTION100
2.6285-2.67160.27641410.24472693X-RAY DIFFRACTION100
2.6716-2.71770.29411400.23962652X-RAY DIFFRACTION100
2.7177-2.76710.33641390.23272642X-RAY DIFFRACTION100
2.7671-2.82030.30731390.23062634X-RAY DIFFRACTION100
2.8203-2.87790.28341410.23052694X-RAY DIFFRACTION100
2.8779-2.94040.29141410.23622664X-RAY DIFFRACTION100
2.9404-3.00880.31111400.23272658X-RAY DIFFRACTION100
3.0088-3.08410.28071410.23042683X-RAY DIFFRACTION100
3.0841-3.16740.28651400.21842665X-RAY DIFFRACTION100
3.1674-3.26060.28181390.21152648X-RAY DIFFRACTION100
3.2606-3.36580.25751430.20682706X-RAY DIFFRACTION100
3.3658-3.48610.26071400.18932672X-RAY DIFFRACTION100
3.4861-3.62560.2311410.1822674X-RAY DIFFRACTION100
3.6256-3.79060.20141420.1722687X-RAY DIFFRACTION100
3.7906-3.99030.18921410.16052679X-RAY DIFFRACTION100
3.9903-4.24020.18871420.1522708X-RAY DIFFRACTION100
4.2402-4.56740.19391440.14752727X-RAY DIFFRACTION100
4.5674-5.02660.18231410.14442688X-RAY DIFFRACTION100
5.0266-5.7530.20271450.16992753X-RAY DIFFRACTION100
5.753-7.24430.20521460.17852771X-RAY DIFFRACTION100
7.2443-48.57040.20541520.15822883X-RAY DIFFRACTION100

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