[English] 日本語
Yorodumi
- PDB-7m93: Bovine sigma-2 receptor bound to PB28 -

+
Open data


ID or keywords:

Loading...

-
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 / 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
(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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more