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- PDB-7v62: Crystal structure of human OSBP ORD in complex with cholesterol -

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Basic information

Entry
Database: PDB / ID: 7v62
TitleCrystal structure of human OSBP ORD in complex with cholesterol
ComponentsOxysterol-binding protein 1
KeywordsLIPID TRANSPORT / Lipid binding protein / Lipid transport protein / Oxysterol binding protein / Oxysterol binding protein-related domain
Function / homology
Function and homology information


positive regulation of secretory granule organization / sterol transfer activity / sphingomyelin biosynthetic process / intracellular cholesterol transport / ceramide transport / sterol binding / sterol transport / perinuclear endoplasmic reticulum / bile acid biosynthetic process / Sphingolipid de novo biosynthesis ...positive regulation of secretory granule organization / sterol transfer activity / sphingomyelin biosynthetic process / intracellular cholesterol transport / ceramide transport / sterol binding / sterol transport / perinuclear endoplasmic reticulum / bile acid biosynthetic process / Sphingolipid de novo biosynthesis / phospholipid transport / oxysterol binding / phosphatidylinositol-4-phosphate binding / positive regulation of insulin secretion involved in cellular response to glucose stimulus / Synthesis of bile acids and bile salts / trans-Golgi network / cell junction / protein domain specific binding / Golgi membrane / endoplasmic reticulum membrane / nucleolus / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / 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. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
CITRIC ACID / CHOLESTEROL / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Oxysterol-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsKobayashi, J. / Kato, R.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)21am0101083j0005 Japan
CitationJournal: Acs Infect Dis. / Year: 2022
Title: Ligand Recognition by the Lipid Transfer Domain of Human OSBP Is Important for Enterovirus Replication.
Authors: Kobayashi, J. / Arita, M. / Sakai, S. / Kojima, H. / Senda, M. / Senda, T. / Hanada, K. / Kato, R.
History
DepositionAug 19, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxysterol-binding protein 1
B: Oxysterol-binding protein 1
C: Oxysterol-binding protein 1
D: Oxysterol-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,64219
Polymers187,6654
Non-polymers2,97715
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.880, 111.880, 367.880
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 405 through 410 or (resid 411...
d_2ens_1(chain "B" and (resid 405 through 413 or (resid 414...
d_3ens_1(chain "C" and (resid 405 through 407 or (resid 408...
d_4ens_1(chain "D" and (resid 405 through 407 or (resid 408...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1PROGLNA2 - 253
d_12ens_1SERILEA259 - 389
d_21ens_1PROILEG1 - 383
d_31ens_1PROGLNK1 - 252
d_32ens_1SERILEK259 - 389
d_41ens_1PROILEP1 - 383

NCS oper:
IDCodeMatrixVector
1given(0.791614128892, 0.610716914231, 0.0192852692557), (-0.606866077063, 0.782164390597, 0.14118226019), (0.0711381434123, -0.123465447613, 0.989795760648)-29.2917439445, 33.2613786622, 43.3669587374
2given(-0.994355067085, -0.105957384303, -0.00557075168333), (-0.104777593555, 0.988847812516, -0.105837892886), (0.0167229319064, -0.104656755125, -0.994367792698)117.163220454, 20.9856471553, 276.725120739
3given(-0.721563614359, -0.692040696203, -0.0206306866885), (-0.69231079579, 0.721513790297, 0.011118113344), (0.00719113805, 0.0223052731683, -0.999725343443)140.789223485, 54.6496571296, 230.511126266

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Oxysterol-binding protein 1


Mass: 46916.195 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: OSBP, OSBP1 / Production host: Homo sapiens (human) / References: UniProt: P22059

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Non-polymers , 5 types, 25 molecules

#2: Chemical
ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: citrate, PEG4000, sodium acetate, GSH/GSSG / PH range: 6.0 - 6.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 3.25→49.6 Å / Num. obs: 37700 / % possible obs: 99.7 % / Redundancy: 28.4 % / Biso Wilson estimate: 86.34 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.99
Reflection shellResolution: 3.25→3.34 Å / Num. unique obs: 6043 / CC1/2: 0.837

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZM8

5zm8


Resolution: 3.25→49.58 Å / SU ML: 0.3762 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.3768
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2524 1884 5 %
Rwork0.2126 35816 -
obs0.2146 37700 99.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.64 Å2
Refinement stepCycle: LAST / Resolution: 3.25→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12440 0 189 10 12639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002912965
X-RAY DIFFRACTIONf_angle_d0.714317610
X-RAY DIFFRACTIONf_chiral_restr0.04661892
X-RAY DIFFRACTIONf_plane_restr0.0052239
X-RAY DIFFRACTIONf_dihedral_angle_d21.93914826
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.27325669003
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.949061315445
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.05340570879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.25-3.340.33641410.31522681X-RAY DIFFRACTION98.77
3.34-3.440.35141420.28262683X-RAY DIFFRACTION98.95
3.44-3.550.28051400.26132670X-RAY DIFFRACTION98.94
3.55-3.670.29541420.24272708X-RAY DIFFRACTION99.2
3.67-3.820.2821410.232693X-RAY DIFFRACTION99.37
3.82-3.990.26951440.22452731X-RAY DIFFRACTION99.41
3.99-4.20.2351430.19812711X-RAY DIFFRACTION99.48
4.21-4.470.23191450.18692760X-RAY DIFFRACTION99.69
4.47-4.810.21091450.18382743X-RAY DIFFRACTION99.93
4.81-5.30.23191460.18352776X-RAY DIFFRACTION99.9
5.3-6.060.25891470.21282800X-RAY DIFFRACTION99.93
6.06-7.630.25821500.212841X-RAY DIFFRACTION99.97
7.63-49.580.22711580.20333019X-RAY DIFFRACTION99.37
Refinement TLS params.Method: refined / Origin x: 57.2721007083 Å / Origin y: 24.7775297438 Å / Origin z: 137.856126801 Å
111213212223313233
T0.395356460431 Å20.0340553700283 Å2-0.0209541254798 Å2-0.289948634548 Å2-0.00726077093612 Å2--0.431113959059 Å2
L0.14552828111 °20.0297546078941 °2-0.300214141938 °2-0.108000372062 °20.0621736826138 °2--1.02403612731 °2
S-0.106982523165 Å °-0.0106411448774 Å °0.0430664620888 Å °-0.00974233624432 Å °-0.0190012837997 Å °0.00791569906886 Å °-0.0192338451271 Å °-0.0141289273473 Å °-2.0320162827E-6 Å °
Refinement TLS groupSelection details: all

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