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- EMDB-8172: Core region of shut state rabbit ryanodine receptor 1 activated b... -

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Basic information

Entry
Database: EMDB / ID: EMD-8172
TitleCore region of shut state rabbit ryanodine receptor 1 activated by calcium ion
Map dataNone
Sample
  • Complex: Ryanodine Receptor 1
    • Protein or peptide: rabbit ryanodine receptor 1
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 / release of sequestered calcium ion into cytosol / muscle contraction / 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
Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsWang X / Wei R / Yin C / Sun F
CitationJournal: Cell Res / Year: 2016
Title: Structural insights into Ca(2+)-activated long-range allosteric channel gating of RyR1.
Authors: Risheng Wei / Xue Wang / Yan Zhang / Saptarshi Mukherjee / Lei Zhang / Qiang Chen / Xinrui Huang / Shan Jing / Congcong Liu / Shuang Li / Guangyu Wang / Yaofang Xu / Sujie Zhu / Alan J ...Authors: Risheng Wei / Xue Wang / Yan Zhang / Saptarshi Mukherjee / Lei Zhang / Qiang Chen / Xinrui Huang / Shan Jing / Congcong Liu / Shuang Li / Guangyu Wang / Yaofang Xu / Sujie Zhu / Alan J Williams / Fei Sun / Chang-Cheng Yin /
Abstract: Ryanodine receptors (RyRs) are a class of giant ion channels with molecular mass over 2.2 mega-Daltons. These channels mediate calcium signaling in a variety of cells. Since more than 80% of the RyR ...Ryanodine receptors (RyRs) are a class of giant ion channels with molecular mass over 2.2 mega-Daltons. These channels mediate calcium signaling in a variety of cells. Since more than 80% of the RyR protein is folded into the cytoplasmic assembly and the remaining residues form the transmembrane domain, it has been hypothesized that the activation and regulation of RyR channels occur through an as yet uncharacterized long-range allosteric mechanism. Here we report the characterization of a Ca(2+)-activated open-state RyR1 structure by cryo-electron microscopy. The structure has an overall resolution of 4.9 Å and a resolution of 4.2 Å for the core region. In comparison with the previously determined apo/closed-state structure, we observed long-range allosteric gating of the channel upon Ca(2+) activation. In-depth structural analyses elucidated a novel channel-gating mechanism and a novel ion selectivity mechanism of RyR1. Our work not only provides structural insights into the molecular mechanisms of channel gating and regulation of RyRs, but also sheds light on structural basis for channel-gating and ion selectivity mechanisms for the six-transmembrane-helix cation channel family.
History
DepositionMay 9, 2016-
Header (metadata) releaseJul 6, 2016-
Map releaseNov 16, 2016-
UpdateNov 16, 2016-
Current statusNov 16, 2016Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.138
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.138
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8172.png

Downloads & links

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Map

FileDownload / File: emd_8172.map.gz / Format: CCP4 / Size: 229.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 392 pix.
= 547.232 Å		1.4 Å/pix.
x 392 pix.
= 547.232 Å		1.4 Å/pix.
x 392 pix.
= 547.232 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.396 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.138 / Movie #1: 0.138
Minimum - Maximum-1.7535816 - 1.1442759
Average (Standard dev.)0.00019829153 (±0.01127109)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions392392392
Spacing392392392
CellA=B=C: 547.232 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3961.3961.396
M x/y/z392392392
origin x/y/z0.0000.0000.000
length x/y/z547.232547.232547.232
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ329329329
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS392392392
D min/max/mean-1.7541.1440.000

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Supplemental data

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Sample components

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Entire : Ryanodine Receptor 1

EntireName: Ryanodine Receptor 1
Components
  • Complex: Ryanodine Receptor 1
    • Protein or peptide: rabbit ryanodine receptor 1

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Supramolecule #1: Ryanodine Receptor 1

SupramoleculeName: Ryanodine Receptor 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 2.2 MDa

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Macromolecule #1: rabbit ryanodine receptor 1

MacromoleculeName: rabbit ryanodine receptor 1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
SequenceString: MGDGGEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAGV ESSQGGGHRT LLYGHAILLR HAHSRMYLSC LTTSRSMTDK LAFDVGLQED ATGEACWWTM HPASKQRSEG EKVRVGDDLI ...String:
MGDGGEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAGV ESSQGGGHRT LLYGHAILLR HAHSRMYLSC LTTSRSMTDK LAFDVGLQED ATGEACWWTM HPASKQRSEG EKVRVGDDLI LVSVSSERYL HLSTASGELQ VDASFMQTLW NMNPICSCCE EGYVTGGHVL RLFHGHMDEC LTISAADSDD QRRLVYYEGG AVCTHARSLW RLEPLRISWS GSHLRWGQPL RIRHVTTGRY LALTEDQGLV VVDACKAHTK ATSFCFRVSK EKLDTAPKRD VEGMGPPEIK YGESLCFVQH VASGLWLTYA APDPKALRLG VLKKKAILHQ EGHMDDALFL TRCQQEESQA ARMIHSTAGL YNQFIKGLDS FSGKPRGSGP PAGPALPIEA VILSLQDLIG YFEPPSEELQ HEEKQSKLRS LRNRQSLFQE EGMLSLVLNC IDRLNVYTTA AHFAEYAGEE AAESWKEIVN LLYELLASLI RGNRANCALF STNLDWVVSK LDRLEASSGI LEVLYCVLIE SPEVLNIIQE NHIKSIISLL DKHGRNHKVL DVLCSLCVCN GVAVRSNQDL ITENLLPGRE LLLQTNLINY VTSIRPNIFV GRAEGSTQYG KWYFEVMVDE VVPFLTAQAT HLRVGWALTE GYSPYPGGGE GWGGNGVGDD LYSYGFDGLH LWTGHVARPV TSPGQHLLAP EDVVSCCLDL SVPSISFRIN GCPVQGVFEA FNLDGLFFPV VSFSAGVKVR FLLGGRHGEF KFLPPPGYAP CHEAVLPRER LRLEPIKEYR REGPRGPHLV GPSRCLSHTD FVPCPVDTVQ IVLPPHLERI REKLAENIHE LWALTRIEQG WTYGPVRDDN KRLHPCLVNF HSLPEPERNY NLQMSGETLK TLLALGCHVG MADEKAEDNL KKTKLPKTYM MSNGYKPAPL DLSHVRLTPA QTTLVDRLAE NGHNVWARDR VAQGWSYSAV QDIPARRNPR LVPYRLLDEA TKRSNRDSLC QAVRTLLGYG YNIEPPDQEP SQVENQSRWD RVRIFRAEKS YTVQSGRWYF EFEAVTTGEM RVGWARPELR PDVELGADEL AYVFNGHRGQ RWHLGSEPFG RPWQSGDVVG CMIDLTENTI IFTLNGEVLM SDSGSETAFR EIEIGDGFLP VCSLGPGQVG HLNLGQDVSS LRFFAICGLQ EGFEPFAINM QRPVTTWFSK SLPQFEPVPP EHPHYEVARM DGTVDTPPCL RLAHRTWGSQ NSLVEMLFLR LSLPVQFHQH FRCTAGATPL APPGLQPPAE DEARAAEPDP DYENLRRSAG GWGEAEGGKE GTAKEGTPGG TPQPGVEAQP VRAENEKDAT TEKNKKRGFL FKAKKAAMMT QPPATPALPR LPHDVVPADN RDDPEIILNT TTYYYSVRVF AGQEPSCVWV GWVTPDYHQH DMNFDLSKVR AVTVTMGDEQ GNVHSSLKCS NCYMVWGGDF VSPGQQGRIS HTDLVIGCLV DLATGLMTFT ANGKESNTFF QVEPNTKLFP AVFVLPTHQN VIQFELGKQK NIMPLSAAMF LSERKNPAPQ CPPRLEVQML MPVSWSRMPN HFLQVETRRA GERLGWAVQC QDPLTMMALH IPEENRCMDI LELSERLDLQ RFHSHTLRLY RAVCALGNNR VAHALCSHVD QAQLLHALED AHLPGPLRAG YYDLLISIHL ESACRSRRSM LSEYIVPLTP ETRAITLFPP GRKGGNARRH GLPGVGVTTS LRPPHHFSPP CFVAALPAAG VAEAPARLSP AIPLEALRDK ALRMLGEAVR DGGQHARDPV GGSVEFQFVP VLKLVSTLLV MGIFGDEDVK QILKMIEPEV FTEEEEEEEE EEEEEEEEEE DEEEKEEDEE EEEKEDAEKE EEEAPEGEKE DLEEGLLQMK LPESVKLQMC NLLEYFCDQE LQHRVESLAA FAERYVDKLQ ANQRSRYALL MRAFTMSAAE TARRTREFRS PPQEQINMLL HFKDEADEED CPLPEDIRQD LQDFHQDLLA HCGIQLEGEE EEPEEETSLS SRLRSLLETV RLVKKKEEKP EEELPAEEKK PQSLQELVSH MVVRWAQEDY VQSPELVRAM FSLLHRQYDG LGELLRALPR AYTISPSSVE DTMSLLECLG QIRSLLIVQM GPQEENLMIQ SIGNIMNNKV FYQHPNLMRA LGMHETVMEV MVNVLGGGET KEIRFPKMVT SCCRFLCYFC RISRQNQRSM FDHLSYLLEN SGIGLGMQGS TPLDVAAASV IDNNELALAL QEQDLEKVVS YLAGCGLQSC PMLLAKGYPD IGWNPCGGER YLDFLRFAVF VNGESVEENA NVVVRLLIRK PECFGPALRG EGGSGLLAAI EEAIRISEDP ARDGPGVRRD RRREHFGEEP PEENRVHLGH AIMSFYAALI DLLGRCAPEM HLIQAGKGEA LRIRAILRSL VPLDDLVGII SLPLQIPTLG KDGALVQPKM SASFVPDHKA SMVLFLDRVY GIENQDFLLH VLDVGFLPDM RAAASLDTAT FSTTEMALAL NRYLCLAVLP LITKCAPLFA GTEHRAIMVD SMLHTVYRLS RGRSLTKAQR DVIEDCLMAL CRYIRPSMLQ HLLRRLVFDV PILNEFAKMP LKLLTNHYER CWKYYCLPTG WANFGVTSEE ELHLTRKLFW GIFDSLAHKK YDQELYRMAM PCLCAIAGAL PPDYVDASYS SKAEKKATVD AEGNFDPRPV ETLNVIIPEK LDSFINKFAE YTHEKWAFDK IQNNWSYGEN VDEELKTHPM LRPYKTFSEK DKEIYRWPIK ESLKAMIAWE WTIEKAREGE EERTEKKKTR KISQTAQTYD PREGYNPQPP DLSGVTLSRE LQAMAEQLAE NYHNTWGRKK KQELEAKGGG THPLLVPYDT LTAKEKARDR EKAQELLKFL QMNGYAVTRG LKDMELDTSS IEKRFAFGFL QQLLRWMDIS QEFIAHLEAV VSSGRVEKSP HEQEIKFFAK ILLPLINQYF TNHCLYFLST PAKVLGSGGH ASNKEKEMIT SLFCKLAALV RHRVSLFGTD APAVVNCLHI LARSLDARTV MKSGPEIVKA GLRSFFESAS EDIEKMVENL RLGKVSQART QVKGVGQNLT YTTVALLPVL TTLFQHIAQH QFGDDVILDD VQVSCYRTLC SIYSLGTTKN TYVEKLRPAL GECLARLAAA MPVAFLEPQL NEYNACSVYT TKSPRERAIL GLPNSVEEMC PDIPVLDRLM ADIGGLAESG ARYTEMPHVI EITLPMLCSY LPRWWERGPE APPPALPAGA PPPCTAVTSD HLNSLLGNIL RIIVNNLGID EATWMKRLAV FAQPIVSRAR PELLHSHFIP TIGRLRKRAG KVVAEEEQLR LEAKAEAEEG ELLVRDEFSV LCRDLYALYP LLIRYVDNNR AHWLTEPNAN AEELFRMVGE IFIYWSKSHN FKREEQNFVV QNEINNMSFL TADSKSKMAK AGDAQSGGSD QERTKKKRRG DRYSVQTSLI VATLKKMLPI GLNMCAPTDQ DLIMLAKTRY ALKDTDEEVR EFLQNNLHLQ GKVEGSPSLR WQMALYRGLP GREEDADDPE KIVRRVQEVS AVLYHLEQTE HPYKSKKAVW HKLLSKQRRR AVVACFRMTP LYNLPTHRAC NMFLESYKAA WILTEDHSFE DRMIDDLSKA GEQEEEEEEV EEKKPDPLHQ LVLHFSRTAL TEKSKLDEDY LYMAYADIMA KSCHLEEGGE NGEAEEEEVE VSFEEKEMEK QRLLYQQSRL HTRGAAEMVL QMISACKGET GAMVSSTLKL GISILNGGNA EVQQKMLDYL KDKKEVGFFQ SIQALMQTCS VLDLNAFERQ NKAEGLGMVN EDGTVINRQN GEKVMADDEF TQDLFRFLQL LCEGHNNDFQ NYLRTQTGNT TTINIIICTV DYLLRLQESI SDFYWYYSGK DVIEEQGKRN FSKAMSVAKQ VFNSLTEYIQ GPCTGNQQSL AHSRLWDAVV GFLHVFAHMM MKLAQDSSQI ELLKELLDLQ KDMVVMLLSL LEGNVVNGMI ARQMVDMLVE SSSNVEMILK FFDMFLKLKD IVGSEAFQDY VTDPRGLISK KDFQKAMDSQ KQFTGPEIQF LLSCSEADEN EMINFEEFAN RFQEPARDIG FNVAVLLTNL SEHVPHDPRL RNFLELAESI LEYFRPYLGR IEIMGASRRI ERIYFEISET NRAQWEMPQV KESKRQFIFD VVNEGGEAEK MELFVSFCED TIFEMQIAAQ ISEPEGEPEA DEDEGMGEAA AEGAEEGAAG AEGAAGTVAA GATARLAAAA ARALRGLSYR SLRRRVRRLR RLTAREAATA LAALLWAVVA RAGAAGAGAA AGALRLLWGS LFGGGLVEGA KKVTVTELLA GMPDPTSDEV HGEQPAGPGG DADGAGEGEG EGDAAEGDGD EEVAGHEAGP GGAEGVVAVA DGGPFRPEGA GGLGDMGDTT PAEPPTPEGS PILKRKLGVD GEEEELVPEP EPEPEPEPEK ADEENGEKEE VPEAPPEPPK KAPPSPPAKK EEAGGAGMEF WGELEVQRVK FLNYLSRNFY TLRFLALFLA FAINFILLFY KVSDSPPGED DMEGSAAGDL AGAGSGGGSG WGSGAGEEAE GDEDENMVYY FLEESTGYME PALWCLSLLH TLVAFLCIIG YNCLKVPLVI FKREKELARK LEFDGLYITE QPGDDDVKGQ WDRLVLNTPS FPSNYWDKFV KRKVLDKHGD IFGRERIAEL LGMDLASLEI TAHNERKPDP PPGLLTWLMS IDVKYQIWKF GVIFTDNSFL YLGWYMVMSL LGHYNNFFFA AHLLDIAMGV KTLRTILSSV THNGKQLVMT VGLLAVVVYL YTVVAFNFFR KFYNKSEDED EPDMKCDDMM TCYLFHMYVG VRAGGGIGDE IEDPAGDEYE LYRVVFDITF FFFVIVILLA IIQGLIIDAF GELRDQQEQV KEDMETKCFI CGIGSDYFDT TPHGFETHTL EEHNLANYMF FLMYLINKDE TEHTGQESYV WKMYQERCWD FFPAGDCFRK QYEDQLS

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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

Concentration5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
300.0 mMNaClsodium chloride
2.0 mMDTTdithiothreitol
2.0 mMPMSFphenylmethanesulfonyl fluoride
20.0 mMHepes4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid

Details: 1:1000 diluted protease inhibitor cocktail was also added in buffer.
GridModel: Quantifoil R2.0/2.0 / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Grids were blotted for 2s before plunging..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.0 K / Max: 80.0 K
Alignment procedureComa free - Residual tilt: 23.0 mrad
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 2-31 / Number grids imaged: 4 / Number real images: 4931 / Average exposure time: 2.0 sec. / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 5.4 µm / Calibrated defocus min: 1.3 µm / Calibrated magnification: 100286 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe 31 frames of each video were processed into 10 images by merging 3 adjacent frames and then subjected into motion correction using program dosefgpu_driftcorr.
Particle selectionNumber selected: 376537
CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

1606


Details: A 60 angstrom low-pass filtered cryo-EM reconstruction of RyR1 (EMDB-1606) was used as an initial mode.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Relion (ver. 1.4)
Details: The particles were used for focused refinement using a local-optimization refinement algorithm to subtract the signal of the peripheral region from the whole density map, which yielded a map ...Details: The particles were used for focused refinement using a local-optimization refinement algorithm to subtract the signal of the peripheral region from the whole density map, which yielded a map of the core region (including the central region containing the U-motif, VSC and CTD and the transmembrane region) at 4.9 Angstrom.
Number images used: 30296
Initial angle assignmentType: OTHER / Software - Name: Relion (ver. 1.4)
Final angle assignmentType: OTHER / Software - Name: Relion (ver. 1.4)
Final 3D classificationNumber classes: 2 / Software - Name: Relion (ver. 1.4)

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Atomic model buiding 1

Initial modelPDB ID:

3j8h


Chain - Chain ID: A / Chain - Residue range: 1-5037
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: MDFF

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