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Yorodumi- EMDB-4295: Structure of Ryanodine Receptor 1 in nanodiscs in the presence of... -
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-Basic information
Entry | Database: EMDB / ID: EMD-4295 | |||||||||
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Title | Structure of Ryanodine Receptor 1 in nanodiscs in the presence of calcium and ATP | |||||||||
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Keywords | calcium release channel / nanodiscs / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / organelle membrane / cellular response to caffeine / outflow tract morphogenesis ...ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / organelle membrane / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / toxic substance binding / voltage-gated calcium channel activity / smooth endoplasmic reticulum / skeletal muscle fiber development / striated muscle contraction / muscle contraction / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / calcium ion transmembrane transport / calcium channel activity / sarcolemma / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 8.2 Å | |||||||||
Authors | Willegems K / Efremov RG | |||||||||
Funding support | Belgium, 2 items
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Citation | Journal: Structure / Year: 2018 Title: Influence of Lipid Mimetics on Gating of Ryanodine Receptor. Authors: Katrien Willegems / Rouslan G Efremov / Abstract: Understanding gating principles of ion channels at high resolution is of great importance. Here we investigate the conformational transition from closed to open state in ryanodine receptor 1 (RyR1) ...Understanding gating principles of ion channels at high resolution is of great importance. Here we investigate the conformational transition from closed to open state in ryanodine receptor 1 (RyR1) reconstituted into lipid nanodiscs. RyR1 is a homotetrameric giant ion channel that couples excitation of muscle cells to fast calcium release from the sarcoplasmic reticulum. Using single-particle cryo-EM we show that RyR1 reconstituted into lipid nanodiscs is stabilized in the open conformation when bound to the plant toxin ryanodine, but not in the presence of its physiological activators, calcium and ATP. Further, using ryanodine binding assays we show that membrane mimetics influence RyR1 transition between closed and open-channel conformations. We find that all detergents, including fluorinated detergents added to nanodiscs, stabilize closed state of RyR1. Our biochemical results correlate with available structural data and suggest optimal conditions for structural studies of RyR1 gating. | |||||||||
History |
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-Structure visualization
Movie |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4295.map.gz | 163.3 MB | EMDB map data format | |
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Header (meta data) | emd-4295-v30.xml emd-4295.xml | 24.6 KB 24.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4295_fsc.xml | 12.3 KB | Display | FSC data file |
Images | emd_4295.png | 133.4 KB | ||
Filedesc metadata | emd-4295.cif.gz | 8.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4295 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4295 | HTTPS FTP |
-Validation report
Summary document | emd_4295_validation.pdf.gz | 297.6 KB | Display | EMDB validaton report |
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Full document | emd_4295_full_validation.pdf.gz | 296.8 KB | Display | |
Data in XML | emd_4295_validation.xml.gz | 12.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4295 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4295 | HTTPS FTP |
-Related structure data
Related structure data | 6fooMC 4258C 6fg3C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4295.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.645 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP
Entire | Name: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP |
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Components |
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-Supramolecule #1: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP
Supramolecule | Name: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / Strain: New Zealand white rabbit / Tissue: skeletal muscle / Location in cell: sarcoplasmic reticulum |
Molecular weight | Theoretical: 2.2 MDa |
-Macromolecule #1: Ryanodine receptor 1
Macromolecule | Name: Ryanodine receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle |
Molecular weight | Theoretical: 532.709688 KDa |
Sequence | String: MGDGGEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSRMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT MHPASKQRSE G EKVRVGDD ...String: MGDGGEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSRMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT MHPASKQRSE G EKVRVGDD LILVSVSSER YLHLSTASGE LQVDASFMQT LWNMNPICSC CEEGYVTGGH VLRLFHGHMD ECLTISAADS DD QRRLVYY EGGAVCTHAR SLWRLEPLRI SWSGSHLRWG QPLRIRHVTT GRYLALTEDQ GLVVVDACKA HTKATSFCFR VSK EKLDTA PKRDVEGMGP PEIKYGESLC FVQHVASGLW LTYAAPDPKA LRLGVLKKKA ILHQEGHMDD ALFLTRCQQE ESQA ARMIH STAGLYNQFI KGLDSFSGKP RGSGPPAGPA LPIEAVILSL QDLIGYFEPP SEELQHEEKQ SKLRSLRNRQ SLFQE EGML SLVLNCIDRL NVYTTAAHFA EYAGEEAAES WKEIVNLLYE LLASLIRGNR ANCALFSTNL DWVVSKLDRL EASSGI LEV LYCVLIESPE VLNIIQENHI KSIISLLDKH GRNHKVLDVL CSLCVCNGVA VRSNQDLITE NLLPGRELLL QTNLINY VT SIRPNIFVGR AEGSTQYGKW YFEVMVDEVV PFLTAQATHL RVGWALTEGY SPYPGGGEGW GGNGVGDDLY SYGFDGLH L WTGHVARPVT SPGQHLLAPE DVVSCCLDLS VPSISFRING CPVQGVFEAF NLDGLFFPVV SFSAGVKVRF LLGGRHGEF KFLPPPGYAP CHEAVLPRER LRLEPIKEYR REGPRGPHLV GPSRCLSHTD FVPCPVDTVQ IVLPPHLERI REKLAENIHE LWALTRIEQ GWTYGPVRDD NKRLHPCLVN FHSLPEPERN YNLQMSGETL KTLLALGCHV GMADEKAEDN LKKTKLPKTY M MSNGYKPA PLDLSHVRLT PAQTTLVDRL AENGHNVWAR DRVAQGWSYS AVQDIPARRN PRLVPYRLLD EATKRSNRDS LC QAVRTLL GYGYNIEPPD QEPSQVENQS RWDRVRIFRA EKSYTVQSGR WYFEFEAVTT GEMRVGWARP ELRPDVELGA DEL AYVFNG HRGQRWHLGS EPFGRPWQSG DVVGCMIDLT ENTIIFTLNG EVLMSDSGSE TAFREIEIGD GFLPVCSLGP GQVG HLNLG QDVSSLRFFA ICGLQEGFEP FAINMQRPVT TWFSKSLPQF EPVPPEHPHY EVARMDGTVD TPPCLRLAHR TWGSQ NSLV EMLFLRLSLP VQF(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) 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(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)MPLSA AMFLSERKNP APQCPPRLEV QMLMPVSWSR MPNHFLQVET RRAGERLGW AVQCQDPLTM MALHIPEENR CMDILELSER LDLQRFHSHT LRLYRAVCAL GNNRVAHALC SHVDQAQLLH A LEDAHLPG PLRAGYYDLL ISIHLESACR SRRSMLSEYI VPLTPETRAI TLFPPGRKGG NARRHGLPGV GVTTSLRPPH HF SPPCFVA ALPAAGVAEA PARLSPAIPL EALRDKALRM LGEAVRDGGQ HARDPVGGSV EFQFVPVLKL VSTLLVMGIF GDE DVKQIL KMIEPEVFTE EEEEEEEEEE EEEEEEEDEE EKEEDEEEEE KEDAEKEEEE APEGEKEDLE EGLLQMKLPE SVKL QMCNL LEYFCDQELQ HRVESLAAFA ERYVDKLQAN QRSRYALLMR AFTMSAAETA RRTREFRSPP QEQINMLLHF KDEAD EEDC PLPEDIRQDL QDFHQDLLAH CGIQLEGEEE EPEEETSLSS RLRSLLETVR LVKKKEEKPE EELPAEEKKP QSLQEL VSH MVVRWAQEDY VQSPELVRAM FSLLHRQYDG LGELLRALPR AYTISPSSVE DTMSLLECLG QIRSLLIVQM GPQEENL MI QSIGNIMNNK VFYQHPNLMR ALGMHETVME VMVNVLGGGE TKEIRFPKMV TSCCRFLCYF CRISRQNQRS MFDHLSYL L ENSGIGLGMQ GSTPLDVAAA SVIDNNELAL ALQEQDLEKV VSYLAGCGLQ SCPMLLAKGY PDIGWNPCGG ERYLDFLRF AVFVNGESVE ENANVVVRLL IRKPECFGPA LRGEGGSGLL AAIEEAIRIS EDPARDGPGV RRDRRREHFG EEPPEENRVH LGHAIMSFY AALIDLLGRC APEMHLIQAG KGEALRIRAI LRSLVPLDDL VGIISLPLQI PTL(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) 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(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) TPLYN LPTHRACNMF LESYKAAWIL TEDHSFEDRM IDDLSKAGEQ EEEEEEVEEK KPDPLHQLVL HFSRTALTEK SKLDE DYLY MAYADIMAKS CHLEEGGENG EAEEEEVEVS FEEKEMEKQR LLYQQSRLHT RGAAEMVLQM ISACKGETGA MVSSTL KLG ISILNGGNAE VQQKMLDYLK DKKEVGFFQS IQALMQTCSV LDLNAFERQN KAEGLGMVNE DGTVINRQNG EKVMADD EF TQDLFRFLQL LCEGHNNDFQ NYLRTQTGNT TTINIIICTV DYLLRLQESI SDFYWYYSGK DVIEEQGKRN FSKAMSVA K QVFNSLTEYI QGPCTGNQQS LAHSRLWDAV VGFLHVFAHM MMKLAQDSSQ IELLKELLDL QKDMVVMLLS LLEGNVVNG MIARQMVDML VESSSNVEMI LKFFDMFLKL KDIVGSEAFQ DYVTDPRGLI SKKDFQKAMD SQKQFTGPEI QFLLSCSEAD ENEMINFEE FANRFQEPAR DIGFNVAVLL TNLSEHVPHD PRLRNFLELA ESILEYFRPY LGRIEIMGAS RRIERIYFEI S ETNRAQWE MPQVKESKRQ FIFDVVNEGG EAEKMELFVS FCEDTIFEMQ IAAQISEPEG EPEADEDEGM GEAAAEGAEE GA AGAEGAA GTVAAGATAR LAAAAARALR GLSYRSLRRR VRRLRRLTAR EAATALAALL WAVVARAGAA GAGAAAGALR LLW GSLFGG GLVEGAKKVT VTELLAGMPD PTSDEVHGEQ PAGPGGDADG AGEGEGEGDA AEGDGDEEVA GHEAGPGGAE GVVA VADGG PFRPEGAGGL GDMGDTTPAE PPTPEGSPIL KRKLGVDGEE EELVPEPEPE PEPEPEKADE ENGEKEEVPE APPEP PKKA PPSPPAKKEE AGGAGMEFWG ELEVQRVKFL NYLSRNFYTL RFLALFLAFA INFILLFYKV SDSPPGEDDM EGSAAG DLA GAGSGGGSGW GSGAGEEAEG DEDENMVYYF LEESTGYMEP ALWCLSLLHT LVAFLCIIGY NCLKVPLVIF KREKELA RK LEFDGLYITE QPGDDDVKGQ WDRLVLNTPS FPSNYWDKFV KRKVLDKHGD IFGRERIAEL LGMDLASLEI TAHNERKP D PPPGLLTWLM SIDVKYQIWK FGVIFTDNSF LYLGWYMVMS LLGHYNNFFF AAHLLDIAMG VKTLRTILSS VTHNGKQLV MTVGLLAVVV YLYTVVAFNF FRKFYNKSED EDEPDMKCDD MMTCYLFHMY VGVRAGGGIG DEIEDPAGDE YELYRVVFDI TFFFFVIVI LLAIIQGLII DAFGELRDQQ EQVKEDMETK CFICGIGSDY FDTTPHGFET HTLEEHNLAN YMFFLMYLIN K DETEHTGQ ESYVWKMYQE RCWDFFPAGD CFRKQYEDQL S UniProtKB: Ryanodine receptor 1, Ryanodine receptor 1, Ryanodine receptor 1, Ryanodine receptor 1 |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3 mg/mL | ||||||||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0004 kPa | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber temperature: 293.15 K / Instrument: HOMEMADE PLUNGER | ||||||||||||||||||||||||
Details | Protein was reconstituted into lipid nanodiscs |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Frames/image: 1-16 / Number grids imaged: 1 / Number real images: 1906 / Average electron dose: 1.7 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 92000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-6foo: |