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- PDB-5u78: Crystal structure of ORP8 PH domain in P1211 space group -

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Basic information

Entry
Database: PDB / ID: 5u78
TitleCrystal structure of ORP8 PH domain in P1211 space group
ComponentsOxysterol-binding protein-related protein 8
KeywordsLIPID TRANSPORT / Oxsyterol / membrane contact site / Phosphoinositide.
Function / homology
Function and homology information


phosphatidylserine acyl-chain remodeling / phosphatidylserine transfer activity / protein localization to nuclear pore / Acyl chain remodelling of PS / : / phospholipid transporter activity / cortical endoplasmic reticulum / phospholipid transport / phosphatidylinositol-4-phosphate binding / cholesterol binding ...phosphatidylserine acyl-chain remodeling / phosphatidylserine transfer activity / protein localization to nuclear pore / Acyl chain remodelling of PS / : / phospholipid transporter activity / cortical endoplasmic reticulum / phospholipid transport / phosphatidylinositol-4-phosphate binding / cholesterol binding / negative regulation of sequestering of triglyceride / phosphatidylserine binding / fat cell differentiation / 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 / intracellular membrane-bounded organelle / 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. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. ...Oxysterol-binding protein / Oxysterol-binding protein, conserved site / Oxysterol-binding protein superfamily / Oxysterol-binding protein / Oxysterol-binding protein family signature. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Oxysterol-binding protein-related protein 8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.978 Å
AuthorsGhai, R. / Yang, H.
Funding support Australia, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1097185 Australia
National Health and Medical Research Council (NHMRC, Australia)1041301 Australia
Australian Research Council (ARC)DP130100457 Australia
CitationJournal: Nat Commun / Year: 2017
Title: ORP5 and ORP8 bind phosphatidylinositol-4, 5-biphosphate (PtdIns(4,5)P 2) and regulate its level at the plasma membrane.
Authors: Ghai, R. / Du, X. / Wang, H. / Dong, J. / Ferguson, C. / Brown, A.J. / Parton, R.G. / Wu, J.W. / Yang, H.
History
DepositionDec 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,4404
Polymers54,4404
Non-polymers00
Water3,531196
1
A: Oxysterol-binding protein-related protein 8


Theoretical massNumber of molelcules
Total (without water)13,6101
Polymers13,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxysterol-binding protein-related protein 8


Theoretical massNumber of molelcules
Total (without water)13,6101
Polymers13,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Oxysterol-binding protein-related protein 8


Theoretical massNumber of molelcules
Total (without water)13,6101
Polymers13,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Oxysterol-binding protein-related protein 8


Theoretical massNumber of molelcules
Total (without water)13,6101
Polymers13,6101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.170, 66.350, 79.549
Angle α, β, γ (deg.)90.00, 94.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 13609.974 Da / Num. of mol.: 4 / Fragment: UNP residues 149-265
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OSBPL8, KIAA1451, ORP8, OSBP10 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS / References: UniProt: Q9BZF1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M Bis-tris propane, pH 6.5, 0.2 M Potassium thiocyanate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.98→40.93 Å / Num. obs: 37677 / % possible obs: 99.2 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U77

5u77


Resolution: 1.978→40.927 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2575 1886 5.02 %
Rwork0.2226 --
obs0.2244 37543 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.978→40.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3739 0 0 196 3935
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123828
X-RAY DIFFRACTIONf_angle_d1.2455179
X-RAY DIFFRACTIONf_dihedral_angle_d15.881397
X-RAY DIFFRACTIONf_chiral_restr0.068585
X-RAY DIFFRACTIONf_plane_restr0.007621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.978-2.03150.34571350.29932698X-RAY DIFFRACTION97
2.0315-2.09130.32061320.26382738X-RAY DIFFRACTION99
2.0913-2.15880.25881500.26612706X-RAY DIFFRACTION99
2.1588-2.23590.33251320.26892707X-RAY DIFFRACTION98
2.2359-2.32540.3551270.31512697X-RAY DIFFRACTION98
2.3254-2.43120.27331350.25112767X-RAY DIFFRACTION99
2.4312-2.55940.27581540.25912728X-RAY DIFFRACTION99
2.5594-2.71970.28231710.23662717X-RAY DIFFRACTION100
2.7197-2.92970.29911460.2522775X-RAY DIFFRACTION100
2.9297-3.22440.27331340.22942785X-RAY DIFFRACTION100
3.2244-3.69070.25111560.20622767X-RAY DIFFRACTION100
3.6907-4.64880.19791610.17222760X-RAY DIFFRACTION100
4.6488-40.93550.22241530.18772812X-RAY DIFFRACTION98
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)
12.3971-1.7093-6.03527.26062.67729.27510.0959-0.0111-0.89160.1667-0.08770.37930.2846-0.73560.20190.30510.0004-0.05850.46780.00570.4651-30.758610.26770.4886
22.02790.7216-1.90311.98578.02586.265-0.617-0.1554-1.36030.18571.2896-1.36060.51211.8375-0.83960.60270.03550.04581.0199-0.43750.8408-14.404411.406-9.9129
36.03322.5872-0.74544.9537-0.31886.0676-0.0931-0.6254-1.12871.0827-0.0870.37040.6648-0.11120.04340.414-0.07560.070.43860.12970.4847-25.668110.01293.9688
49.29510.24144.24632.3055-6.72253.0023-0.4589-0.1809-0.35540.52040.71-0.319-0.4034-0.5216-0.22270.37870.01680.05290.43020.00120.2448-23.079920.06463.5738
56.19243.2381.93218.55482.86855.3657-0.12250.98840.2058-1.56560.24920.32120.2937-0.02520.020.6047-0.0362-0.06470.66350.05060.3691-25.66318.7895-12.7967
65.2352-1.98743.07472.0766-7.6639.0218-0.0455-0.1950.00671.21570.17830.2494-1.3096-0.0450.00930.3709-0.01170.02580.2792-0.09570.3542-18.493226.8867-1.09
75.62090.5956-0.95886.7205-3.63988.40530.1279-1.1356-0.6591.0066-0.1873-0.346-0.36550.15010.43710.3504-0.0559-0.09350.58040.11130.4095-15.94115.35035.5617
82.22762.31862.29067.16631.8016.6393-0.42820.9243-1.5586-0.12870.6389-0.11660.3209-0.2052-0.04420.3742-0.03850.01590.4513-0.14250.4755-23.537213.358-9.7288
99.3767-0.24960.55133.47344.92792.8588-0.04981.32881.0775-0.95690.2823-0.1111-0.6978-0.731-0.09720.4922-0.0320.0230.63940.20710.6058-34.135218.357-6.4741
109.80140.0744-3.62335.5245-0.65474.5591-0.21480.5426-0.5346-0.485-0.0605-1.09480.2105-0.09650.30830.26720.06580.02370.2008-0.04280.418.0673-0.573-40.2316
112.1032.15968.64322.0472-0.87537.7995-0.7646-0.3527-0.67630.74630.98341.0483-0.2529-0.6139-0.32410.31790.02810.05920.33850.10580.2637-8.6296-0.0169-30.0594
125.5875-0.3573-0.42565.9539-0.54062.99910.38910.4846-0.6613-0.9104-0.35150.10590.15130.1197-0.01760.36340.0894-0.00220.2539-0.12760.34663.0869-0.756-43.7826
136.4321-0.07082.93426.83540.72053.256-0.2511-0.02130.643-0.1834-0.0831-0.0248-0.35030.0560.19820.16760.01120.06720.2191-0.03110.32441.988610.6939-37.8535
142.3406-2.89190.67322.0576-1.61835.98720.0424-0.6948-4.22960.9049-1.62190.06880.7428-0.36850.40550.6061-0.11370.10180.9928-0.4464-0.01610.85270.186-21.2563
157.855-7.17982.9563.278-5.32569.6737-0.4996-0.7592-0.00140.01450.7433-0.47850.2048-0.1156-0.16610.23450.0372-0.05790.20420.0060.31181.79939.1733-29.8961
164.6356-0.13940.77248.54560.45334.6160.26790.8730.0057-1.2582-0.62990.92650.1437-0.01180.10620.3280.1301-0.07550.3117-0.0280.3072-4.59710.057-45.1384
178.596-0.6911.69861.1781-0.82325.22410.1664-0.1626-0.4226-0.1282-0.12090.06150.51640.0825-0.0050.20340.0378-0.03020.2018-0.01970.2584-3.583.4565-33.1708
189.6563-0.007-1.21423.60480.22473.6226-0.4786-0.71240.76730.58080.5687-1.3671-0.31790.3853-0.1330.26130.0592-0.08330.3984-0.20710.432311.39387.432-33.0882
197.2783-0.30951.1695.3609-0.79533.3358-0.0854-0.90980.89150.6663-0.06680.96250.2512-0.2025-0.16330.30510.05310.06230.4046-0.0010.2938-2.64677.82141.4763
208.5306-1.4565-1.43638.65881.73794.60020.0567-0.2220.5875-0.2860.27820.051-0.3682-0.1626-0.19670.29280.04910.02860.2926-0.01110.25122.62747.9446-1.2168
215.5816-2.5017-0.98326.4105-2.17765.7694-0.3362-0.9723-0.37310.6120.37290.3946-0.0326-0.3329-0.10020.27980.02050.02470.50460.03870.30372.6526-3.65216.4182
227.93023.05182.16197.3536-2.88292.1580.01080.58020.1334-0.56030.0334-0.21430.49790.32650.20890.26080.04530.07910.28810.05430.28878.70431.4655-6.0535
232.41512.3482-4.42962.46835.51465.6530.6824-0.5817-0.0001-0.3447-0.46620.2383-0.7834-0.3742-0.31180.51270.0720.03490.4487-0.02910.20423.97773.728.5846
248.74430.84580.20754.4697-0.41646.1813-0.473-2.0552-1.68610.99220.49830.5486-0.0509-0.5781-0.04370.41670.15470.10780.79640.29320.492-7.80330.87517.6353
258.0509-0.18592.61563.8423.10387.0415-0.009-0.2122-0.0345-0.2548-0.04430.2729-0.1057-0.21210.11260.21790.04460.03930.14990.05060.3043-26.098829.8053-38.9044
269.0799-1.60121.6225.75010.8453.9770.03390.30880.92820.00470.0716-0.0526-0.02080.6052-0.2560.19260.02880.02130.22970.05310.3159-18.258730.2198-36.2561
273.6306-0.97990.3884.98622.14121.7171.35051.16760.9811-1.5492-1.7667-0.1389-0.102-1.2195-0.10330.36150.4942-0.0120.04580.4640.5266-22.29730.1925-45.7093
286.3626-1.6506-1.97196.5924-0.52953.6598-0.03290.1654-0.3846-0.04840.2530.46410.2421-0.3225-0.39250.1450.0212-0.04270.20250.0430.3004-21.670518.8368-37.8817
29-0.0488-0.1088-0.0606-0.04710.0291-0.0605-0.6829-1.26190.8820.64-0.06720.1572-0.357-0.5564-0.08891.0875-0.0144-0.36541.03650.28790.8243-22.201728.7971-21.0806
302.924-7.6801-3.60763.1234.41877.8034-0.4935-0.1199-0.14760.8272-0.03340.49680.1441-0.7941-0.11510.29490.06180.0260.2959-0.03370.3271-21.426720.2265-29.8467
316.4006-1.6705-1.23729.5034-4.42675.90810.5640.5358-0.4775-0.7093-0.6765-0.16710.44120.18190.10160.26680.05640.00130.1656-0.05970.4533-15.241114.3203-40.3027
322.8477-0.81381.47063.5505-2.49316.94190.27770.92280.6665-1.1129-0.6874-1.24770.03620.490.31840.39050.19430.22620.42060.17330.4963-13.038125.2742-44.9434
332.35112.1971-3.53242.31153.07433.52770.2792-0.0760.3374-0.4226-0.49140.0785-0.7882-0.4724-0.04270.23990.0737-0.04520.3337-0.02790.1831-20.335127.224-29.8885
349.18020.3432-0.27532.87732.12728.7829-0.0614-0.4184-1.04160.35760.15410.9140.2574-0.69060.00280.22750.0531-0.03570.32110.14730.5013-31.071322.1161-33.0631
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 17 )
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 46 )
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 55 )
5X-RAY DIFFRACTION5chain 'A' and (resid 56 through 73 )
6X-RAY DIFFRACTION6chain 'A' and (resid 74 through 83 )
7X-RAY DIFFRACTION7chain 'A' and (resid 84 through 101 )
8X-RAY DIFFRACTION8chain 'A' and (resid 102 through 109 )
9X-RAY DIFFRACTION9chain 'A' and (resid 110 through 127 )
10X-RAY DIFFRACTION10chain 'B' and (resid 6 through 17 )
11X-RAY DIFFRACTION11chain 'B' and (resid 18 through 24 )
12X-RAY DIFFRACTION12chain 'B' and (resid 25 through 46 )
13X-RAY DIFFRACTION13chain 'B' and (resid 47 through 60 )
14X-RAY DIFFRACTION14chain 'B' and (resid 61 through 67 )
15X-RAY DIFFRACTION15chain 'B' and (resid 68 through 74 )
16X-RAY DIFFRACTION16chain 'B' and (resid 75 through 94 )
17X-RAY DIFFRACTION17chain 'B' and (resid 95 through 109 )
18X-RAY DIFFRACTION18chain 'B' and (resid 110 through 127 )
19X-RAY DIFFRACTION19chain 'C' and (resid 7 through 18 )
20X-RAY DIFFRACTION20chain 'C' and (resid 19 through 46 )
21X-RAY DIFFRACTION21chain 'C' and (resid 47 through 79 )
22X-RAY DIFFRACTION22chain 'C' and (resid 80 through 99 )
23X-RAY DIFFRACTION23chain 'C' and (resid 100 through 109 )
24X-RAY DIFFRACTION24chain 'C' and (resid 110 through 126 )
25X-RAY DIFFRACTION25chain 'D' and (resid 6 through 18 )
26X-RAY DIFFRACTION26chain 'D' and (resid 19 through 32 )
27X-RAY DIFFRACTION27chain 'D' and (resid 33 through 46 )
28X-RAY DIFFRACTION28chain 'D' and (resid 47 through 60 )
29X-RAY DIFFRACTION29chain 'D' and (resid 61 through 67 )
30X-RAY DIFFRACTION30chain 'D' and (resid 68 through 74 )
31X-RAY DIFFRACTION31chain 'D' and (resid 75 through 84 )
32X-RAY DIFFRACTION32chain 'D' and (resid 85 through 101 )
33X-RAY DIFFRACTION33chain 'D' and (resid 102 through 109 )
34X-RAY DIFFRACTION34chain 'D' and (resid 110 through 127 )

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