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- PDB-7m95: Bovine sigma-2 receptor bound to Z1241145220 -

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Basic information

Entry
Database: PDB / ID: 7m95
TitleBovine sigma-2 receptor bound to Z1241145220
ComponentsSigma intracellular receptor 2
KeywordsMEMBRANE PROTEIN / receptor / sterol / dimer
Function / homology
Function and homology information


regulation of intracellular lipid transport / regulation of intracellular cholesterol transport / positive regulation of lipoprotein transport / rough endoplasmic reticulum membrane / oxysterol binding / positive regulation of wound healing / cholesterol binding / rough endoplasmic reticulum / cholesterol homeostasis / nuclear membrane ...regulation of intracellular lipid transport / regulation of intracellular cholesterol transport / positive regulation of lipoprotein transport / rough endoplasmic reticulum membrane / oxysterol binding / positive regulation of wound healing / cholesterol binding / rough endoplasmic reticulum / cholesterol homeostasis / nuclear membrane / lysosome / endoplasmic reticulum / plasma membrane
Similarity search - Function
Sigma intracellular receptor 2 / EXPERA domain / EXPERA (EXPanded EBP superfamily) / EXPERA domain profile.
Similarity search - Domain/homology
CHOLESTEROL / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Chem-ZNC / Sigma intracellular receptor 2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsAlon, A. / Kruse, A.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM119185 United States
CitationJournal: Nature / Year: 2021
Title: Structures of the sigma 2 receptor enable docking for bioactive ligand discovery.
Authors: Alon, A. / Lyu, J. / Braz, J.M. / Tummino, T.A. / Craik, V. / O'Meara, M.J. / Webb, C.M. / Radchenko, D.S. / Moroz, Y.S. / Huang, X.P. / Liu, Y. / Roth, B.L. / Irwin, J.J. / Basbaum, A.I. / ...Authors: Alon, A. / Lyu, J. / Braz, J.M. / Tummino, T.A. / Craik, V. / O'Meara, M.J. / Webb, C.M. / Radchenko, D.S. / Moroz, Y.S. / Huang, X.P. / Liu, Y. / Roth, B.L. / Irwin, J.J. / Basbaum, A.I. / Shoichet, B.K. / Kruse, A.C.
History
DepositionMar 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 5, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 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

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Assembly

Deposited unit
A: Sigma intracellular receptor 2
B: Sigma intracellular receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,69014
Polymers40,4602
Non-polymers4,23012
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-19 kcal/mol
Surface area16900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.368, 61.539, 110.411
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Sigma intracellular receptor 2 / Sigma-2 receptor / Sigma2 receptor / Transmembrane protein 97


Mass: 20229.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: TMEM97, S2R / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3MHW7
#2: Chemical ChemComp-ZNC / 3-[1-(3-phenylpropyl)-1,2,3,6-tetrahydropyridin-4-yl]-1H-pyrrolo[2,3-b]pyridine


Mass: 317.427 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H23N3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CLR / CHOLESTEROL


Mass: 386.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O
#4: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C21H40O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.16 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6 / Details: PEG 300,0.1 M MES pH 6,210 mM ammonium phosphate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033167 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 11, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.41→49.5 Å / Num. obs: 15203 / % possible obs: 99.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 48.8 Å2 / CC1/2: 0.996 / Rsym value: 0.184 / Net I/σ(I): 7.5
Reflection shellResolution: 2.41→2.55 Å / Mean I/σ(I) obs: 0.7 / Num. unique obs: 2375 / CC1/2: 0.352 / % possible all: 98.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
XDSdata reduction
XDSdata scaling
Cootmodel building
PHENIX1.18.2_3874refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7M93

7m93


Resolution: 2.41→49.49 Å / SU ML: 0.3477 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5621
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2459 1063 7.01 %
Rwork0.2136 14102 -
obs0.2159 15165 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.03 Å2
Refinement stepCycle: LAST / Resolution: 2.41→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 196 46 2986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353041
X-RAY DIFFRACTIONf_angle_d0.73964106
X-RAY DIFFRACTIONf_chiral_restr0.0406434
X-RAY DIFFRACTIONf_plane_restr0.0053536
X-RAY DIFFRACTIONf_dihedral_angle_d18.45211185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.41-2.510.37061270.33031682X-RAY DIFFRACTION97.1
2.52-2.650.34061310.29151739X-RAY DIFFRACTION99.84
2.65-2.810.30491310.24341744X-RAY DIFFRACTION99.95
2.81-3.030.26721310.22241727X-RAY DIFFRACTION100
3.03-3.340.24731320.21371756X-RAY DIFFRACTION99.95
3.34-3.820.25171330.19371776X-RAY DIFFRACTION100
3.82-4.810.20661360.18351792X-RAY DIFFRACTION99.79
4.81-49.490.22221420.21071886X-RAY DIFFRACTION99.8

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