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- PDB-7m93: Bovine sigma-2 receptor bound to PB28 -

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Basic information

Entry
Database: PDB / ID: 7m93
TitleBovine sigma-2 receptor bound to PB28
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 / PB28 / Sigma intracellular receptor 2
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 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)87,03721
Polymers80,9204
Non-polymers6,11717
Water48627
1
A: Sigma intracellular receptor 2
B: Sigma intracellular receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,05312
Polymers40,4602
Non-polymers3,59310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-18 kcal/mol
Surface area16740 Å2
MethodPISA
2
C: Sigma intracellular receptor 2
D: Sigma intracellular receptor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9849
Polymers40,4602
Non-polymers2,5247
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2030 Å2
ΔGint-22 kcal/mol
Surface area15610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.597, 55.174, 92.985
Angle α, β, γ (deg.)90.000, 95.050, 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 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q3MHW7
#2: Chemical
ChemComp-YT1 / PB28 / 1-cyclohexyl-4-{3-[(1R)-5-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]propyl}piperazine


Mass: 370.571 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H38N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: agonist*YM
#3: Chemical
ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C21H40O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6 / Details: PEG 300, 0.1 M MES pH 6, 600 mM NaCl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.254858 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.254858 Å / Relative weight: 1
ReflectionResolution: 2.94→33.88 Å / Num. obs: 15228 / % possible obs: 98.67 % / Redundancy: 4 % / Biso Wilson estimate: 55.95 Å2 / CC1/2: 0.974 / Rpim(I) all: 0.118 / Rrim(I) all: 0.227 / Net I/σ(I): 5.73
Reflection shellResolution: 2.94→3.047 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 0.93 / Num. unique obs: 760 / CC1/2: 0.495 / Rpim(I) all: 0.585 / % possible all: 90.76

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OHT

6oht


Resolution: 2.94→33.88 Å / SU ML: 0.4102 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 24.5834
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2498 1524 10.01 %
Rwork0.199 13704 -
obs0.2043 15228 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.28 Å2
Refinement stepCycle: LAST / Resolution: 2.94→33.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5446 0 339 28 5813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335984
X-RAY DIFFRACTIONf_angle_d0.59398076
X-RAY DIFFRACTIONf_chiral_restr0.0381860
X-RAY DIFFRACTIONf_plane_restr0.00471000
X-RAY DIFFRACTIONf_dihedral_angle_d11.10712329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.94-3.040.3261250.27831122X-RAY DIFFRACTION89.97
3.04-3.150.3151340.25281209X-RAY DIFFRACTION98.97
3.15-3.270.29581440.2281289X-RAY DIFFRACTION99.72
3.27-3.420.29581360.23731232X-RAY DIFFRACTION99.85
3.42-3.60.29021390.22321251X-RAY DIFFRACTION99.43
3.6-3.830.27371380.19591236X-RAY DIFFRACTION99.85
3.83-4.120.24391380.17811250X-RAY DIFFRACTION99.64
4.12-4.530.23851420.18691267X-RAY DIFFRACTION99.86
4.53-5.190.20311400.16641265X-RAY DIFFRACTION99.86
5.19-6.530.21081420.20051274X-RAY DIFFRACTION99.86
6.53-33.880.2261460.17941309X-RAY DIFFRACTION99.11
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)
12.965166356080.8777476370082.397975548422.805340970321.32284340638.28559109326-0.0454062293443-0.10321035125-0.1934169858750.1693380150870.155006862170.120205962373-0.3631990295580.103149112006-0.1868258523410.300773226629-0.0507482481090.04492851493710.3712025656740.06223953213870.4369861901476.86994173362-25.856851893532.4290753253
23.66973992905-0.90530302965-2.990651394196.337067044663.341090466123.615839434770.08883375634520.4002392261060.249813945943-0.3651348900970.2572863554830.210389716459-0.8233640239450.640594104835-0.2275699777810.517252876975-0.0846509093336-0.162306801960.6340414586670.1102632995710.505546098927-7.2108034744-30.766181545623.1739338576
37.970455845485.76778505591-7.819486068854.82994970554-6.690327116489.28514813551-0.5254635371220.64372918855-1.01775516537-1.01131113831-0.120932733651-0.4446327164150.596029284429-0.349040003970.6816145411930.544621754610.041826060653-0.07677924990250.430251761599-0.07817054407910.389800373211-8.6751890551-19.34413170623.2360439869
45.17646377421-1.868837336950.7255576954934.57323147197-1.542989022951.5656232849-0.6772941077530.738930340355-0.1055393292790.131172070707-0.133840891292-0.351319837546-0.3046738864230.3833727495060.7057339367880.349653600441-0.02002984866580.0899368379490.4100842575450.04703207021580.30511168411710.3050873635-18.376103020131.2709877064
57.37186909857-0.805571907725-0.8504651025161.21883301245-0.3491572156831.254461850910.1478505672660.173237759622-0.4859103754320.292130347083-0.0775569178252-0.06245512727750.160895057833-0.03113573125640.07968686435330.326999981447-0.002335325436320.04494395900480.297771153498-0.005015735916090.246085400874.66896002409-12.487349054836.9767774823
68.020839258378.779692574716.751052058111.999012963089.451532605638.05899842907-1.130160288380.5744802440931.02335244239-1.620170473640.2162665644941.83241423096-1.361133956790.3000818257390.2335082656180.4398752345240.09311386785120.08233662581630.4132657574-0.0824018097530.896935488189-18.1406767255-15.31356350525.0097977438
75.13309850138-2.16527749139-0.2569623583013.243532437820.2887351580716.97091311280.202363086656-0.5871896782960.0936455756987-0.836257785868-0.1062623482110.5917845507180.653023153426-1.28288613103-0.005640016876510.570707557432-0.0270143438474-0.05236231809090.5144664802230.04175773557010.24254491911-12.7856394494-21.590414073735.7267325511
88.793638574093.287388958622.265817727816.781589487570.4495298062932.841342201770.483828802196-0.08001877363530.3375185421120.690036709383-0.460724379520.2316172889110.2785714167950.3666976855890.006227496236320.355464343790.01229171843250.1216472821950.4046353515420.07093011335380.2734370051755.37394056643-15.790617907344.1389298804
92.645898661310.856866405644-1.313687197412.918512320271.845169106582.63594839751.17547894524-1.48124048067-0.8340070480621.17200782941-1.31503653976-1.20051537709-0.0849676133885-0.9105792662010.2451639663610.7487427729990.0694439855452-0.2098378263231.105399536110.1526706800110.83418476608718.7902804755-14.765075668251.0299476393
106.995935167011.01913056439-1.16022881412.04836673448-0.6967017258472.652023153930.01593377774830.5971659867021.13303833377-0.142125429085-0.04113945859850.304029015107-0.333875106130.1949320210880.06020443859130.5128126937530.0342109736931-0.03479255459590.3035463863910.09705897214270.3247770394988.5180731302411.554223139836.0126790697
113.20570374513-0.424968448813-1.480138577794.90657899454-1.66805799247.349930787630.06340945631470.137057359869-0.0759991213313-0.1875342987770.0140242794190.34521220498-0.88147060574-0.467717731079-0.2129285171240.5556425749020.0116995061647-0.02662814266910.437642988780.01924846135520.295646394915-12.331353920713.395493975629.3422300183
127.920194270337.25298800145-8.351691666317.81869611797-7.99078626348.901709513031.03036806109-0.6592796662220.307160874304-0.324000831460.9891371451752.235717297911.05057219242-2.41924241733-1.067737822130.434623881424-0.155508767548-0.2393719826360.591797392932-0.06287632733640.725240857905-10.18326581433.1424097635623.9461138196
134.282678106243.6930824866-0.3338904521634.273635092921.212837848842.974935826570.100306439364-0.591850411657-0.02123743527840.0229634884731-0.125372179196-0.21730165957-0.403566584164-0.2606319442460.01012376002820.3567473112090.02906528400940.005850898968210.2923097045130.0131821751640.4024817166172.799313470613.7717431227740.0265219332
144.66444911220.02094622987612.883612958322.46506490895-0.09690888817048.80268957234-0.02401494889640.5708656112460.5219652905250.474304974324-0.3493365976190.1622069257970.1931496753380.6777569007310.2856271525560.23159169187-0.01850406624640.04104261343590.294453538517-0.002929036557220.2429947147856.93291949792-2.1106097859833.0534514853
154.55256996008-6.32627394253-4.914655209859.040889244597.140198511765.68810290933-0.1381984600371.58337111006-1.029230976341.95903699969-0.7605318236470.6278064122492.46567739991-1.415851042780.7972616509170.768996696938-0.114394385262-0.007218417025350.768405372236-0.07073024905050.461311296382-13.1697001482-3.0770428184515.4542341197
164.80769934492-2.561265325875.772484862533.27566362327-2.879009335117.17401911740.2121663478550.6253164939660.312918410539-0.18049749098-0.28080505194-0.08166285045510.2237926082750.6110841267720.04330345591480.2527941554150.004740477091390.03742742113970.4995388825110.04627668229940.3238113489197.917578041423.244969856825.7490632107
173.46350941016-1.194436926661.012723209192.25287979934-2.641804083474.67061727211-0.273521411547-0.192706901816-0.4441448379590.3208196276380.108399302224-0.237448389511-0.924308761946-0.2886322340130.1254767438490.3577474450040.00149123007320.02591309851850.326576409899-0.04014259333430.49386774846626.99729922012.7766115010516.317467656
180.981134906516-0.434467475015-1.553415570844.344227053382.597871645834.50952982551-0.024439561043-0.2305250052140.4598909569630.0946986497033-0.1811085166520.44232959197-0.167784707956-0.4522998208090.1351091464890.266209618305-0.007465345646780.03441153485450.3024707166060.04833711629530.23653475132223.405345080711.617970873215.7130201792
199.03001028733-2.568992794963.428189253685.13227878883-0.3755877975945.365402434760.04201250986080.4424231376650.0328190057684-0.0973368966922-0.165077553322-0.1178625968530.1391948028550.2570804725410.05728304315580.311738910666-0.05601811365460.09555625331320.373367177743-0.0367994860840.20213516705131.239775221414.5953282358.10587512642
207.288653394440.231016616843-2.279408211483.90456414568-1.527892757951.478004485530.0920887531498-0.6177590324280.2787685622170.07640842134770.0526784973459-0.0285265900584-0.341143679586-0.374631289917-0.1533450219950.4031662749710.04803374589650.03794529971930.519645322765-0.07769024298670.20127941665228.351089340441.27217250019.35158393495
217.917865910554.98113000318-4.759627898668.89484014347-4.608077182469.26553426345-0.08399035940080.0385628300729-0.5598068190220.6379316300940.000105884550857-1.11875505088-0.9672872240620.9525089594420.04894163207820.522236105479-0.0324704428689-0.04115770876220.374325188549-0.07065848809870.37570835329840.016737720344.857412778821.7084852028
226.20867920101-6.86739866929-5.144228813368.98575890585.585392725874.262572726340.623962958747-0.04462807169321.30481276606-0.3740961524090.957949649864-2.117192149110.4583676082621.48166032381-1.589576185340.451795872301-0.02245226515550.05649993323080.505852780085-0.07473758681960.37461954406239.179213112733.074217456723.2724024065
230.9009221870410.602533335083-0.7772721295243.49682400728-1.98250956361.314939133650.05336237325320.3022397305950.250097923966-0.05294563311790.2147995758820.278749144589-0.377774694723-0.0143132096822-0.2993274378320.2832102732720.0925787837104-0.002598665206410.480451564197-0.02064407267690.34788736162225.643385535831.2323485678.6683855956
249.159326454775.324986455245.087139425547.634414695024.520511981283.36347033060.7759232418340.238128091395-1.443104413171.030391538810.872346173435-1.472138602070.6565756190870.99999804963-1.692913653270.6242426244340.146308443594-0.007735623923370.80730787617-0.1135441160610.64352672876839.489097275429.395739417532.1222907586
254.858835565020.524815604299-0.1441861334224.642247278280.1228606426984.85738571247-0.214857459635-0.4320582723470.781224827104-0.242612732275-0.05769834751190.0275563713025-0.472144737491-0.9073601257620.282029998520.1600841242980.02484022254740.08478890104490.409560743470.0166289480920.43129889656119.414286207933.584781064717.5555404866
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 4 through 40 )AA4 - 401 - 37
22chain 'A' and (resid 41 through 54 )AA41 - 5438 - 51
33chain 'A' and (resid 55 through 63 )AA55 - 6352 - 60
44chain 'A' and (resid 64 through 93 )AA64 - 9361 - 90
55chain 'A' and (resid 94 through 120 )AA94 - 12091 - 117
66chain 'A' and (resid 121 through 136 )AA121 - 136118 - 133
77chain 'A' and (resid 137 through 147 )AA137 - 147134 - 144
88chain 'A' and (resid 148 through 163 )AA148 - 163145 - 160
99chain 'A' and (resid 164 through 168 )AA164 - 168161 - 165
1010chain 'B' and (resid 3 through 32 )BI3 - 321 - 30
1111chain 'B' and (resid 33 through 54 )BI33 - 5431 - 52
1212chain 'B' and (resid 55 through 63 )BI55 - 6353 - 61
1313chain 'B' and (resid 64 through 93 )BI64 - 9362 - 91
1414chain 'B' and (resid 94 through 120 )BI94 - 12092 - 118
1515chain 'B' and (resid 121 through 130 )BI121 - 130119 - 128
1616chain 'B' and (resid 131 through 167 )BI131 - 167129 - 165
1717chain 'C' and (resid 5 through 54 )CM5 - 541 - 50
1818chain 'C' and (resid 55 through 93 )CM55 - 9351 - 89
1919chain 'C' and (resid 94 through 167 )CM94 - 16790 - 159
2020chain 'D' and (resid 5 through 40 )DR5 - 401 - 36
2121chain 'D' and (resid 41 through 54 )DR41 - 5437 - 50
2222chain 'D' and (resid 55 through 63 )DR55 - 6351 - 59
2323chain 'D' and (resid 64 through 120 )DR64 - 12060 - 116
2424chain 'D' and (resid 121 through 136 )DR121 - 136117 - 132
2525chain 'D' and (resid 137 through 167 )DR137 - 167133 - 163

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