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- PDB-8p7a: Crystal structure of the ORD domain of human ORP8 -

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Basic information

Entry
Database: PDB / ID: 8p7a
TitleCrystal structure of the ORD domain of human ORP8
ComponentsOxysterol-binding protein-related protein 8
KeywordsLIPID TRANSPORT / oxysterol-binding protein-related protein 8 / lipid / transport
Function / homology
Function and homology information


phosphatidylserine acyl-chain remodeling / phosphatidylserine transfer activity / Acyl chain remodelling of PS / : / protein localization to nuclear pore / phospholipid transporter activity / cortical endoplasmic reticulum / phospholipid transport / phosphatidylinositol-4-phosphate binding / negative regulation of sequestering of triglyceride ...phosphatidylserine acyl-chain remodeling / phosphatidylserine transfer activity / Acyl chain remodelling of PS / : / protein localization to nuclear pore / phospholipid transporter activity / cortical endoplasmic reticulum / phospholipid transport / phosphatidylinositol-4-phosphate binding / negative regulation of sequestering of triglyceride / cholesterol binding / fat cell differentiation / phosphatidylserine binding / positive regulation of insulin receptor signaling pathway / negative regulation of cell migration / positive regulation of glucose import / nuclear membrane / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endoplasmic reticulum membrane / endoplasmic reticulum / 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. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Oxysterol-binding protein-related protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsEisenreichova, A. / Klima, M. / Boura, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cells / Year: 2023
Title: Crystal Structure of the ORP8 Lipid Transport ORD Domain: Model of Lipid Transport.
Authors: Eisenreichova, A. / Klima, M. / Anila, M.M. / Koukalova, A. / Humpolickova, J. / Rozycki, B. / Boura, E.
History
DepositionMay 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxysterol-binding protein-related protein 8
B: Oxysterol-binding protein-related protein 8


Theoretical massNumber of molelcules
Total (without water)88,6022
Polymers88,6022
Non-polymers00
Water00
1
A: Oxysterol-binding protein-related protein 8


Theoretical massNumber of molelcules
Total (without water)44,3011
Polymers44,3011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxysterol-binding protein-related protein 8


Theoretical massNumber of molelcules
Total (without water)44,3011
Polymers44,3011
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.610, 190.240, 58.720
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Oxysterol-binding protein-related protein 8 / ORP-8 / OSBP-related protein 8


Mass: 44300.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OSBPL8, KIAA1451, ORP8, OSBP10 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9BZF1

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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: 3.33 Å3/Da / Density % sol: 63.05 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 15% PEG 20.000, 100 mM HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.56→47.56 Å / Num. obs: 38965 / % possible obs: 52.87 % / Redundancy: 12.9 % / Biso Wilson estimate: 34.29 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.2847 / Rpim(I) all: 0.08174 / Rrim(I) all: 0.2964 / Net I/σ(I): 9.52
Reflection shellResolution: 2.56→2.652 Å / Redundancy: 12.3 % / Rmerge(I) obs: 4.747 / Mean I/σ(I) obs: 0.51 / Num. unique obs: 130 / CC1/2: 0.495 / CC star: 0.814 / Rpim(I) all: 1.398 / Rrim(I) all: 4.952 / % possible all: 3.39

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Processing

Software
NameVersionClassification
XDSxdsapp v2.0data reduction
XDSxdsapp v2.0data scaling
PHASER2.8.3phasing
Coot0.9.8.7model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.56→47.56 Å / SU ML: 0.2924 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.5722
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 1016 4.92 %random selection
Rwork0.219 19615 --
obs0.2206 20631 52.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.3 Å2
Refinement stepCycle: LAST / Resolution: 2.56→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5597 0 0 0 5597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00325760
X-RAY DIFFRACTIONf_angle_d0.58617817
X-RAY DIFFRACTIONf_chiral_restr0.0462831
X-RAY DIFFRACTIONf_plane_restr0.00621003
X-RAY DIFFRACTIONf_dihedral_angle_d11.55332083
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.690.4031120.3737219X-RAY DIFFRACTION4.21
2.69-2.860.3458240.3747630X-RAY DIFFRACTION11.96
2.86-3.080.2889570.33071281X-RAY DIFFRACTION24.22
3.08-3.390.33711350.28582557X-RAY DIFFRACTION48.77
3.39-3.880.27762140.22924089X-RAY DIFFRACTION76.89
3.88-4.890.22382810.19295303X-RAY DIFFRACTION99.27
4.89-47.560.22742930.19885536X-RAY DIFFRACTION99.47

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