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- 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
TitleStructure of Ryanodine Receptor 1 in nanodiscs in the presence of calcium and ATP
Map data
Sample
  • Complex: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP
    • Protein or peptide: Ryanodine receptor 1
  • Ligand: ZINC ION
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 / cellular response to caffeine / intracellularly gated calcium channel activity / 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 / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis / organelle membrane / toxic substance binding / voltage-gated calcium channel activity / skeletal muscle fiber development / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / muscle contraction / sarcoplasmic reticulum / calcium ion transmembrane transport / calcium channel activity / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / membrane / identical protein binding
Similarity search - Function
: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain ...: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / RyR/IP3 receptor binding core, RIH domain superfamily / : / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Rabbit (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsWillegems K / Efremov RG
Funding support Belgium, 2 items
OrganizationGrant numberCountry
IWT131261 Belgium
FWOG.0266.15N Belgium
CitationJournal: 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
DepositionFeb 8, 2018-
Header (metadata) releaseMay 9, 2018-
Map releaseAug 8, 2018-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6foo
  • Surface level: 0.08
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4295.png

Downloads & links

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Map

FileDownload / File: emd_4295.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.645 Å
Density
Contour LevelBy AUTHOR: 0.08 / Movie #1: 0.08
Minimum - Maximum-0.15258141 - 0.2814365
Average (Standard dev.)-0.0002147259 (±0.012860419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 592.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.6451.6451.645
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z592.200592.200592.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1530.281-0.000

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Supplemental data

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Sample components

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Entire : Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP

EntireName: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP
Components
  • Complex: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP
    • Protein or peptide: Ryanodine receptor 1
  • Ligand: ZINC ION

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Supramolecule #1: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP

SupramoleculeName: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Strain: New Zealand white rabbit / Tissue: skeletal muscle / Location in cell: sarcoplasmic reticulum
Molecular weightTheoretical: 2.2 MDa

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Macromolecule #1: Ryanodine receptor 1

MacromoleculeName: Ryanodine receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit) / Tissue: skeletal muscle
Molecular weightTheoretical: 532.709688 KDa
SequenceString: 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) (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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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) 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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) (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) 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

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMC7H15NO4S3-morpholinopropane-1-sulfonic acid
200.0 mMNaClSodium chloridesodium chloride
7.0 mMC10H16N5O13P3Adenosine triphosphate
1.0 mMC4H10O2S2Dithiothreitol
0.2 mMC14H24N2O10EGTA
0.25 mMCaCl2calcium chloride
2.0 mg/mLC20H25F13O11fluorinated octyl maltoside
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.0004 kPa
VitrificationCryogen name: ETHANE / Chamber temperature: 293.15 K / Instrument: HOMEMADE PLUNGER
DetailsProtein was reconstituted into lipid nanodiscs

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 92000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-16 / Number grids imaged: 1 / Number real images: 1906 / Average electron dose: 1.7 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 90000
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Initial angle assignmentType: PROJECTION MATCHING
Final 3D classificationSoftware - Name: RELION (ver. 2.1)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 42500
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL
Output model

PDB-6foo:
Structure of Ryanodine Receptor 1 in nanodiscs in the presence of calcium and ATP

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