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- EMDB-73035: Consensus map of RyR-toxin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-73035
TitleConsensus map of RyR-toxin complex
Map data
Sample
  • Complex: Complex between Ryanodine Receptor 1 and FKBP12.6
    • Complex: Ryanodine receptor 1
      • Protein or peptide: Ryanodine Receptor 1
    • Complex: Peptidyl-prolyl cis-trans isomerase FKBP1B
      • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
KeywordsIon channel / Complex / Activation / MEMBRANE PROTEIN
Function / homology
Function and homology information


negative regulation of calcium-mediated signaling / ATP-gated ion channel activity / negative regulation of release of sequestered calcium ion into cytosol / response to redox state / ryanodine-sensitive calcium-release channel activity / terminal cisterna / negative regulation of heart rate / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine ...negative regulation of calcium-mediated signaling / ATP-gated ion channel activity / negative regulation of release of sequestered calcium ion into cytosol / response to redox state / ryanodine-sensitive calcium-release channel activity / terminal cisterna / negative regulation of heart rate / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine / skin development / ryanodine receptor complex / FK506 binding / 'de novo' protein folding / organelle membrane / outflow tract morphogenesis / smooth endoplasmic reticulum / intracellularly gated calcium channel activity / regulation of ryanodine-sensitive calcium-release channel activity / toxic substance binding / calcium channel inhibitor activity / skeletal muscle fiber development / voltage-gated calcium channel activity / release of sequestered calcium ion into cytosol / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel complex / cellular response to calcium ion / muscle contraction / sarcoplasmic reticulum membrane / calcium-mediated signaling / calcium channel regulator activity / peptidylprolyl isomerase / sarcoplasmic reticulum / peptidyl-prolyl cis-trans isomerase activity / striated muscle contraction / protein refolding / sarcolemma / intracellular calcium ion homeostasis / protein maturation / calcium channel activity / Z disc / Stimuli-sensing channels / calcium ion transmembrane transport / disordered domain specific binding / protein folding / calmodulin binding / protein homotetramerization / transmembrane transporter binding / signaling receptor binding / calcium ion binding / ATP binding / membrane / identical protein binding / cytoplasm
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 / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / 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 / Peptidyl-prolyl cis-trans isomerase domain superfamily / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 1 / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.87 Å
AuthorsZhang Y / Yuchi Z / Van Petegem F
Funding support Canada, China, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-159601 Canada
Chinese Scholarship Council202306250027 China
CitationJournal: To Be Published
Title: Structure of RyR1-toxin complex
Authors: Zhang Y / Yuchi Z / Van Petegem F
History
DepositionOct 5, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73035.png

Downloads & links

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Map

FileDownload / File: emd_73035.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 512 pix.
= 476.16 Å		0.93 Å/pix.
x 512 pix.
= 476.16 Å		0.93 Å/pix.
x 512 pix.
= 476.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.93 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0276
Minimum - Maximum-0.29174307 - 0.5134307
Average (Standard dev.)0.00022260104 (±0.0087736845)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 476.16 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_73035_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_73035_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex between Ryanodine Receptor 1 and FKBP12.6

EntireName: Complex between Ryanodine Receptor 1 and FKBP12.6
Components
  • Complex: Complex between Ryanodine Receptor 1 and FKBP12.6
    • Complex: Ryanodine receptor 1
      • Protein or peptide: Ryanodine Receptor 1
    • Complex: Peptidyl-prolyl cis-trans isomerase FKBP1B
      • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B

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Supramolecule #1: Complex between Ryanodine Receptor 1 and FKBP12.6

SupramoleculeName: Complex between Ryanodine Receptor 1 and FKBP12.6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 11 KDa

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Supramolecule #2: Ryanodine receptor 1

SupramoleculeName: Ryanodine receptor 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Supramolecule #3: Peptidyl-prolyl cis-trans isomerase FKBP1B

SupramoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ryanodine Receptor 1

MacromoleculeName: 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

UniProtKB: Ryanodine receptor 1

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Macromolecule #2: Peptidyl-prolyl cis-trans isomerase FKBP1B

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GVEIETISPG DGRTFPKKGQ TCVVHYTGML QNGKKFDSSR DRNKPFKFRI GKQEVIKGFE EGAAQMSLGQ RAKLTCTPDV AYGATGHPGV IPPNATLIFD VELLNLE

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B

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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

Concentration12 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
Details50 mM HEPES pH 7.5 + 500 mM NaCl + 2 mM EGTA + 2 mM TCEP + 0.1 mM PMSF + 0.5% CHAPS + 0.2% soybean phosphatidylcholine + 1:1000 protease inhibitor cocktail

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 8121 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 343385
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.2) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6m2w

Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.2) / Number images used: 185628
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.2)
FSC plot (resolution estimation)

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