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- PDB-5zm8: Crystal structure of ORP2-ORD in complex with PI(4,5)P2 -

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Basic information

Entry
Database: PDB / ID: 5zm8
TitleCrystal structure of ORP2-ORD in complex with PI(4,5)P2
ComponentsOxysterol-binding protein-related protein 2
KeywordsLIPID TRANSPORT / Transporter / Complex / Phospholipid
Function / homology
Function and homology information


phosphatidylinositol transfer activity / intracellular cholesterol transport / regulation of synaptic vesicle priming / bile acid biosynthetic process / plasma membrane organization / perinuclear endoplasmic reticulum / phospholipid transport / cholesterol transfer activity / cholesterol transport / cholesterol binding ...phosphatidylinositol transfer activity / intracellular cholesterol transport / regulation of synaptic vesicle priming / bile acid biosynthetic process / plasma membrane organization / perinuclear endoplasmic reticulum / phospholipid transport / cholesterol transfer activity / cholesterol transport / cholesterol binding / Synthesis of bile acids and bile salts / phosphatidylinositol-4,5-bisphosphate binding / lipid droplet / cytoplasmic side of plasma membrane / protein homotetramerization / glutamatergic synapse / plasma membrane / cytosol
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-IEP / Oxysterol-binding protein-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, H. / Dong, J.Q. / Wang, J. / Wu, J.W.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2016YFA0502004 China
CitationJournal: Mol. Cell / Year: 2019
Title: ORP2 Delivers Cholesterol to the Plasma Membrane in Exchange for Phosphatidylinositol 4, 5-Bisphosphate (PI(4,5)P2).
Authors: Wang, H. / Ma, Q. / Qi, Y. / Dong, J. / Du, X. / Rae, J. / Wang, J. / Wu, W.F. / Brown, A.J. / Parton, R.G. / Wu, J.W. / Yang, H.
History
DepositionApr 1, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 2, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxysterol-binding protein-related protein 2
B: Oxysterol-binding protein-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,6414
Polymers105,5472
Non-polymers2,0942
Water2,792155
1
A: Oxysterol-binding protein-related protein 2
hetero molecules

A: Oxysterol-binding protein-related protein 2
hetero molecules

A: Oxysterol-binding protein-related protein 2
hetero molecules

A: Oxysterol-binding protein-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,2838
Polymers211,0954
Non-polymers4,1884
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation5_756-x+2,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
Buried area15760 Å2
ΔGint-78 kcal/mol
Surface area65450 Å2
MethodPISA
2
B: Oxysterol-binding protein-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8212
Polymers52,7741
Non-polymers1,0471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.160, 156.160, 199.221
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Oxysterol-binding protein-related protein 2 / OSBP-related protein 2


Mass: 52773.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OSBPL2, KIAA0772, ORP2 / Plasmid: pET-Duet / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9H1P3
#2: Chemical ChemComp-IEP / [(2~{S})-1-octadecanoyloxy-3-[oxidanyl-[(1~{R},2~{R},3~{S},4~{S},5~{S},6~{S})-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] icosa-5,8,11,14-tetraenoate


Mass: 1047.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H85O19P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM MES pH 6.5, 50mM MgCl2, 8% isopropanol, 1.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 34082 / % possible obs: 100 % / Redundancy: 9.9 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.042 / Rrim(I) all: 0.129 / Χ2: 0.961 / Net I/σ(I): 17.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 4.38 / Num. unique obs: 1676 / CC1/2: 0.932 / Rpim(I) all: 0.198 / Rrim(I) all: 0.588 / Χ2: 0.947 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZM5

5zm5


Resolution: 2.7→42.322 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2543 1686 5.09 %
Rwork0.2159 --
obs0.2178 33119 97.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→42.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6543 0 138 155 6836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086872
X-RAY DIFFRACTIONf_angle_d1.0789296
X-RAY DIFFRACTIONf_dihedral_angle_d22.4892605
X-RAY DIFFRACTIONf_chiral_restr0.12967
X-RAY DIFFRACTIONf_plane_restr0.0041176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6995-2.7790.34721100.28292098X-RAY DIFFRACTION79
2.779-2.86860.29111410.27292354X-RAY DIFFRACTION89
2.8686-2.97110.28271510.2612583X-RAY DIFFRACTION98
2.9711-3.09010.29571550.25872659X-RAY DIFFRACTION100
3.0901-3.23070.30421450.2422658X-RAY DIFFRACTION100
3.2307-3.40090.31751270.24112681X-RAY DIFFRACTION100
3.4009-3.61390.26191320.22122688X-RAY DIFFRACTION100
3.6139-3.89270.24911480.21022692X-RAY DIFFRACTION100
3.8927-4.28410.21871320.18962703X-RAY DIFFRACTION100
4.2841-4.90330.20231430.17892721X-RAY DIFFRACTION100
4.9033-6.17450.24071570.20132740X-RAY DIFFRACTION100
6.1745-42.32760.23311450.19842856X-RAY DIFFRACTION99

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