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- PDB-7m94: Bovine sigma-2 receptor bound to Roluperidone -

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Basic information

Entry
Database: PDB / ID: 7m94
TitleBovine sigma-2 receptor bound to Roluperidone
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 / cholesterol binding / positive regulation of wound healing / 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 / cholesterol binding / positive regulation of wound healing / 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
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Roluperidone / Sigma intracellular receptor 2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)89,87329
Polymers80,9204
Non-polymers8,95325
Water18010
1
A: Sigma intracellular receptor 2
B: Sigma intracellular receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,47116
Polymers40,4602
Non-polymers5,01114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-20 kcal/mol
Surface area15870 Å2
MethodPISA
2
C: Sigma intracellular receptor 2
D: Sigma intracellular receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,40213
Polymers40,4602
Non-polymers3,94211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-20 kcal/mol
Surface area16010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.050, 54.161, 99.699
Angle α, β, γ (deg.)90.000, 91.093, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: TMEM97, S2R / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3MHW7
#2: Chemical
ChemComp-YT7 / Roluperidone / 2-({1-[2-(4-fluorophenyl)-2-oxoethyl]piperidin-4-yl}methyl)-2,3-dihydro-1H-isoindol-1-one / MIN-101 / Roluperidone


Mass: 366.429 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H23FN2O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: antagonist*YM
#3: Chemical...
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6
Details: PEG 300, 0.1 M MES pH 6, 500 mM NaCl, 60 mM succinate

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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 17, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033167 Å / Relative weight: 1
ReflectionResolution: 2.71→49.84 Å / Num. obs: 20340 / % possible obs: 99.54 % / Redundancy: 6.8 % / Biso Wilson estimate: 65.09 Å2 / CC1/2: 0.994 / Net I/σ(I): 5.9
Reflection shellResolution: 2.71→2.81 Å / Num. unique obs: 3222 / CC1/2: 0.366 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX1.19.1_4122refinement
Blu-Icedata collection
XDSdata reduction
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7M93
Resolution: 2.71→49.84 Å / SU ML: 0.4044 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.9758
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2537 2004 9.85 %
Rwork0.2127 18336 -
obs0.2167 20340 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.52 Å2
Refinement stepCycle: LAST / Resolution: 2.71→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5467 0 358 10 5835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036016
X-RAY DIFFRACTIONf_angle_d0.6228111
X-RAY DIFFRACTIONf_chiral_restr0.0373857
X-RAY DIFFRACTIONf_plane_restr0.00481052
X-RAY DIFFRACTIONf_dihedral_angle_d13.05152297
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.770.38461310.34681259X-RAY DIFFRACTION95.8
2.77-2.850.31471480.30111317X-RAY DIFFRACTION99.86
2.85-2.930.34521390.29011278X-RAY DIFFRACTION100
2.93-3.030.3531400.27611307X-RAY DIFFRACTION99.93
3.03-3.140.34341470.28141313X-RAY DIFFRACTION99.86
3.14-3.260.28831400.25781286X-RAY DIFFRACTION99.93
3.26-3.410.29851410.241305X-RAY DIFFRACTION99.93
3.41-3.590.25991420.22721313X-RAY DIFFRACTION100
3.59-3.810.22421470.19481316X-RAY DIFFRACTION99.93
3.81-4.110.20151470.18581301X-RAY DIFFRACTION99.72
4.11-4.520.21981370.18381328X-RAY DIFFRACTION99.86
4.52-5.170.23211450.17571316X-RAY DIFFRACTION99.86
5.18-6.520.26391440.22741328X-RAY DIFFRACTION100
6.52-49.840.22691560.17631369X-RAY DIFFRACTION99.09
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.72159558951-0.5816944643890.2854787236151.6889837782-0.1612821126070.8020548737540.32947094274-0.02911506121870.64417239103-0.07162109619510.46857273163-0.650449063912-0.4270365956830.23283176173-0.03926086501590.684155350257-0.0174014971410.00548833030290.647100058774-0.02725831021430.67227149198644.441264812137.325209770416.2639165497
22.43698608551-1.43612189038-0.7698547589314.512840221164.189440524214.081137078080.0811815368517-0.234385871819-0.509407657231-0.3775102585361.10449604324-0.3426203587650.1076977908560.32066549367-0.1809562974630.7804036310580.102451875227-0.1024443349320.7465127262470.2203940545090.80017561220342.788813017227.512750930722.2964403494
31.27509908716-0.5117358217210.4105410012712.18997346681-0.0755313496333.41028253180.2401159402661.202023913080.1369129319550.0678586369828-0.326788330276-0.131339145237-0.2909076624580.2123595403250.02765748641110.572677567499-0.006741682891510.00679677920520.6271967560360.02266997358020.36821966179928.303710113428.22450137566.82678602561
41.819285566020.371993432527-1.600905970052.19931171519-0.06213873879881.32408771767-0.08089545103050.2291385013690.434193126641-0.0145847836724-0.239173504847-0.157387583946-0.182393617291-0.06438575107280.01982671156450.362985168420.02907940127280.02318751651930.4070897403420.01226951321220.44431863985227.39386375622.289600319616.8919915416
50.711859290663-0.2697073546440.8569614177481.853664229-0.8319192108561.158005144380.0218795854892-0.764815304493-0.673757859828-0.6723234837190.155721837471-0.477413618439-0.1312418176230.742882512810.008000210088380.86785098689-0.0129828443865-0.1994722625330.917484558118-0.08522519811060.91620009748445.188631710724.043009369330.8107008171
61.305242215420.6625240358381.430183729421.56258696323-0.5142793202423.031899924230.00807081627423-0.533427251369-0.2787974236660.119057648936-0.0309792150629-0.146631407651-0.609551525316-0.616192637583-2.651038686430.301192176590.09859990753430.06856600989590.410073121265-0.01682072201850.41219029778521.400018528427.921215430119.5199176784
71.088235396360.450530642779-0.7158509818391.950101800850.8814302235682.28030126693-0.603747345899-0.4639262902790.4926132169990.932753407323-0.2244728296010.257777173849-0.3676796831050.6145402275860.3177971969920.7546626146940.1849523938850.08734333423340.6196123646710.0281276239890.54980903731713.6338325527-26.645044405244.2580454583
80.2237968032030.56343249629-0.03501936759171.243294214740.351461235464-0.146082364491-0.332339092779-0.0167093306745-0.065523186303-0.0490290449570.3168710952010.1625741219630.1515500315690.2698296321970.07635818034260.5215159814960.02103272009790.002352145323230.49365584480.01129217171470.5995868374220.921254062791-22.50120081425.3370950251
90.788764230140.657983595569-0.09641819133911.721633645410.7415141757372.01668556045-0.3614416621420.122891329637-0.08945266575730.3397540141550.243689475651-0.2942516365550.4211944510880.5103917306730.1412748133420.4858483105820.128576808978-0.009755991757820.563308676112-0.005365110945230.49272718416412.7299359645-16.262360708140.3887895535
105.53133130576-0.6155099110880.658414751421.466989796910.1123216509181.48453368470.348967997822-0.7064032237080.4147066097560.0354400296267-0.3402654478880.1427518540110.345086105607-0.296593028805-0.05292697742070.567136069261-0.004085676061970.05133845191110.4434836168780.03531574664020.482822053145-0.375415031054-17.404481443641.5844537267
112.281720490510.22100170133-0.5057286295813.26146248029-0.1815281466050.6474789261290.0577491354173-0.0765970314703-0.0920584700987-0.01952211823480.1036473893160.237009934999-0.1410651810790.12800001436-0.102820949350.44974768393-0.01591014574960.006650570540440.40046597901-0.01158944442710.3757256130743.108569530225.2545534234736.3571503833
121.49859329919-0.188902775354-1.534172612412.404097061380.6179900803521.51224691717-0.009680163700180.517719531457-0.0290841306462-0.02801006328180.346959876898-0.0422852327043-0.6175961222390.481502311411-0.1808058414780.3553738390240.0632587617021-0.05316366595570.415873968052-0.08856843694230.52559310468111.25920717643.4854693130929.4279682511
131.053858526710.0310408716913-1.006117975261.98804820744-0.642062817871.25408771874-0.09621480282420.157317268399-0.1305429143950.0566388373526-0.0402471715624-0.3100513572070.399341849812-0.192956158491-0.09909469007580.59537320876-0.08397746718930.1486873879670.517799683349-0.04008818069780.61270229496527.74593074891.1912082561117.8107992704
143.582266110771.14886617190.5908165548841.14760327316-0.127784744321.235023724870.175072844999-0.522636616829-0.5758759163180.332985028354-0.1458218337180.06057152332920.340779956242-0.3268293408090.04276295646320.54883445964-0.02808261477040.0721723997730.601693416757-0.07333874228090.40780611148926.896962778912.096864953210.3682930244
151.38153835815-0.143448281029-0.1323957518310.05277712693150.1046800499160.201173210083-1.05996487461-0.3176137645221.326617291881.568321409180.543876465021-0.3707908419410.5542076928331.080983694090.01498368138051.02441610799-0.09060929648140.04283183024951.05213979586-0.05497625269531.3275690338250.15631266369.9097862859719.4961054427
161.037081559430.755733383947-0.1915049747291.007938375350.6645026740811.290135153310.01532268350480.9463019583170.130493413755-0.0239066399044-0.14505675029-0.1072228747610.01074313208860.0671508677907-0.09785306611410.634204613736-0.04173019455590.051102819420.58619329464-0.06546915495520.58338722036230.21175769226.65104175055.08941752716
170.4384643062850.8289171325790.04526522246341.580499501130.554490987720.500491228811-0.2540013490890.2290127413660.4401479022160.2817681037030.1749609836440.221420649696-0.190170517877-0.2983968192570.07567219098190.618816155203-0.0002961543153260.03607309945940.5830012166530.05039678923170.49560596562222.972076819136.236113458311.1088592795
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'D' and (resid 33 through 54 )DW33 - 5431 - 52
22chain 'D' and (resid 55 through 63 )DW55 - 6353 - 61
33chain 'D' and (resid 64 through 93 )DW64 - 9362 - 91
44chain 'D' and (resid 94 through 125 )DW94 - 12592 - 123
55chain 'D' and (resid 126 through 136 )DW126 - 136124 - 134
66chain 'D' and (resid 137 through 168 )DW137 - 168135 - 166
77chain 'A' and (resid 2 through 27 )AA2 - 271 - 26
88chain 'A' and (resid 28 through 76 )AA28 - 7627 - 75
99chain 'A' and (resid 77 through 120 )AA77 - 12076 - 119
1010chain 'A' and (resid 121 through 168 )AA121 - 168120 - 163
1111chain 'B' and (resid 3 through 130 )BE3 - 1301 - 128
1212chain 'B' and (resid 131 through 167 )BE131 - 167129 - 165
1313chain 'C' and (resid 4 through 93 )CQ4 - 931 - 90
1414chain 'C' and (resid 94 through 120 )CQ94 - 12091 - 117
1515chain 'C' and (resid 121 through 136 )CQ121 - 136118 - 133
1616chain 'C' and (resid 137 through 168 )CQ137 - 168134 - 165
1717chain 'D' and (resid 3 through 32 )DW3 - 321 - 30

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