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- EMDB-43304: Structure of mouse RyR1 in complex with S100A1 (high-Ca2+/CFF/ATP... -
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Open data
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Basic information
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Title | Structure of mouse RyR1 in complex with S100A1 (high-Ca2+/CFF/ATP dataset) | |||||||||
![]() | Mouse RyR1 in complex with S100A1 (high-Ca/CFF/ATP dataset) | |||||||||
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![]() | Calcium / Ion Channel / MEMBRANE PROTEIN | |||||||||
Function / homology | ![]() junctional membrane complex / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / mTORC1-mediated signalling / regulation of response to osmotic stress / cytoplasmic side of membrane / regulation of muscle contraction / sarcoplasmic reticulum calcium ion transport / transforming growth factor beta receptor binding / Stimuli-sensing channels ...junctional membrane complex / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / mTORC1-mediated signalling / regulation of response to osmotic stress / cytoplasmic side of membrane / regulation of muscle contraction / sarcoplasmic reticulum calcium ion transport / transforming growth factor beta receptor binding / Stimuli-sensing channels / type I transforming growth factor beta receptor binding / Ion homeostasis / heart trabecula formation / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / S100 protein binding / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to caffeine / ossification involved in bone maturation / ventricular cardiac muscle tissue morphogenesis / skin development / cellular response to ATP / regulation of heart contraction / organelle membrane / FK506 binding / cellular response to caffeine / positive regulation of sprouting angiogenesis / outflow tract morphogenesis / extrinsic component of cytoplasmic side of plasma membrane / regulation of ryanodine-sensitive calcium-release channel activity / smooth endoplasmic reticulum / voltage-gated calcium channel activity / skeletal muscle fiber development / striated muscle contraction / muscle contraction / heart morphogenesis / T cell proliferation / axon terminus / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / T-tubule / sarcoplasmic reticulum membrane / calcium channel complex / Hsp70 protein binding / cellular response to calcium ion / sarcomere / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / calcium channel activity / cytoplasmic side of plasma membrane / sarcolemma / Z disc / cytokine-mediated signaling pathway / calcium ion transport / ATPase binding / protease binding / protein homotetramerization / vesicle / transmembrane transporter binding / calmodulin binding / synapse / calcium ion binding / perinuclear region of cytoplasm / Golgi apparatus / enzyme binding / protein homodimerization activity / protein-containing complex / mitochondrion / nucleoplasm / ATP binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.56 Å | |||||||||
![]() | Weninger G / Marks AR | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into the regulation of RyR1 by S100A1. Authors: Gunnar Weninger / Marco C Miotto / Carl Tchagou / Steven Reiken / Haikel Dridi / Sören Brandenburg / Gabriel C Riedemann / Qi Yuan / Yang Liu / Alexander Chang / Anetta Wronska / Stephan E ...Authors: Gunnar Weninger / Marco C Miotto / Carl Tchagou / Steven Reiken / Haikel Dridi / Sören Brandenburg / Gabriel C Riedemann / Qi Yuan / Yang Liu / Alexander Chang / Anetta Wronska / Stephan E Lehnart / Andrew R Marks / ![]() ![]() Abstract: S100A1, a small homodimeric EF-hand Ca-binding protein (~21 kDa), plays an important regulatory role in Ca signaling pathways involved in various biological functions including Ca cycling and ...S100A1, a small homodimeric EF-hand Ca-binding protein (~21 kDa), plays an important regulatory role in Ca signaling pathways involved in various biological functions including Ca cycling and contractile performance in skeletal and cardiac myocytes. One key target of the S100A1 interactome is the ryanodine receptor (RyR), a huge homotetrameric Ca release channel (~2.3 MDa) of the sarcoplasmic reticulum. Here, we report cryoelectron microscopy structures of S100A1 bound to RyR1, the skeletal muscle isoform, in absence and presence of Ca. Ca-free apo-S100A1 binds beneath the bridging solenoid (BSol) and forms contacts with the junctional solenoid and the shell-core linker of RyR1. Upon Ca-binding, S100A1 undergoes a conformational change resulting in the exposure of the hydrophobic pocket known to serve as a major interaction site of S100A1. Through interactions of the hydrophobic pocket with RyR1, Ca-bound S100A1 intrudes deeper into the RyR1 structure beneath BSol than the apo-form and induces sideways motions of the C-terminal BSol region toward the adjacent RyR1 protomer resulting in tighter interprotomer contacts. Interestingly, the second hydrophobic pocket of the S100A1-dimer is largely exposed at the hydrophilic surface making it prone to interactions with the local environment, suggesting that S100A1 could be involved in forming larger heterocomplexes of RyRs with other protein partners. Since S100A1 interactions stabilizing BSol are implicated in the regulation of RyR-mediated Ca release, the characterization of the S100A1 binding site conserved between RyR isoforms may provide the structural basis for the development of therapeutic strategies regarding treatments of RyR-related disorders. | |||||||||
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 38.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.8 KB 22.8 KB | Display Display | ![]() |
Images | ![]() | 70.1 KB | ||
Filedesc metadata | ![]() | 9.8 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8vk4MC ![]() 8vjjC ![]() 8vjkC ![]() 8vk3C C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Mouse RyR1 in complex with S100A1 (high-Ca/CFF/ATP dataset) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.833 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
-Entire : Complex of RyR1 with Calstabin-1 and S100A1 (high-Ca2+/CFF/ATP co...
Entire | Name: Complex of RyR1 with Calstabin-1 and S100A1 (high-Ca2+/CFF/ATP condition) |
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Components |
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-Supramolecule #1: Complex of RyR1 with Calstabin-1 and S100A1 (high-Ca2+/CFF/ATP co...
Supramolecule | Name: Complex of RyR1 with Calstabin-1 and S100A1 (high-Ca2+/CFF/ATP condition) type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 / Details: 0.25 mM free Ca2+; 5 mM Caffeine; 10 mM ATP |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: Peptidyl-prolyl cis-trans isomerase FKBP1A
Macromolecule | Name: Peptidyl-prolyl cis-trans isomerase FKBP1A / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.939629 KDa |
Sequence | String: MGVQVETISP GDGRTFPKRG QTCVVHYTGM LEDGKKFDSS RDRNKPFKFT LGKQEVIRGW EEGVAQMSVG QRAKLIISSD YAYGATGHP GIIPPHATLV FDVELLKLE UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1A |
-Macromolecule #2: Protein S100A1
Macromolecule | Name: Protein S100A1 / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 10.516784 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGSELESAME TLINVFHAHS GKEGDKYKLS KKELKDLLQT ELSGFLDVQK DADAVDKVMK ELDENGDGEV DFKEYVVLVA ALTVACNNF FWETS UniProtKB: Protein S100 |
-Macromolecule #3: Ryanodine receptor 1
Macromolecule | Name: Ryanodine receptor 1 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 565.692562 KDa |
Sequence | String: MGDGGGEGED EVQFLRTDDE VVLQCSATVL KEQLKLCLAA EGFGNRLCFL EPTSNAQNVP PDLAICCFIL EQSLSVRALQ EMLANTVEA GVESSQGGGH RTLLYGHAIL LRHAHSRMYL SCLTTSRSMT DKLAFDVGLQ EDATGEACWW TMHPASKQRS E GEKVRVGD ...String: MGDGGGEGED EVQFLRTDDE VVLQCSATVL KEQLKLCLAA EGFGNRLCFL EPTSNAQNVP PDLAICCFIL EQSLSVRALQ EMLANTVEA GVESSQGGGH RTLLYGHAIL LRHAHSRMYL SCLTTSRSMT DKLAFDVGLQ EDATGEACWW TMHPASKQRS E GEKVRVGD DLILVSVSSE RYLHLSTASG ELQVDASFMQ TLWNMNPICS GCEEGFVTGG HVLRLFHGHM DECLTISPSD SD DQRRLVY YEGGPVCTHA RSLWRLEPLR ISWSGSHLRW GQPLRIRHVT TGRYLGLTED QGLVVVDASK AHTKATSFCF RIS KEKLDV APKRDVEGMG PPEIKYGESL CFVQHVASGL WLTYAAPDPK ALRLGVLKKK AMLHQEGHMD DALSLTRCQQ EESQ AARMI YSTAGLYNQF IKGLDSFSGK PRGSGPPAGS ALPIEGVILS LQDLIGYFEP PSEELQHEEK QTKLRSLRNR QSLFQ EEGM LSLVLNCIDR LNVYTTAAHF AEFAGEEAAE SWKEIVNLLY ELLASLIRGN RTNCALFSTN LDWLVSKLDR LEASSG ILE VLYCVLIESP EVLNIIQENH IKSIISLLDK HGRNHKVLDV LCSLCVCNGV AVRSNQDLIT ENLLPGRELL LQTNLIN YV TSIRPNIFVG RAEGSTQYGK WYFEVMVDEV APFLTAQATH LRVGWALSEG YSPYPGGGEG WGGNGVGDDL YSYGFDGL H LWTGHVARPV TSPGQHLLAP EDVVSCCLDL SVPSISFRIN GCPVQGVFES FNLDGLFFPV VSFSAGIKVR FLLGGRHGE FKFLPPPGYA PCHEAVLPRE RLHLQPIKEY RREGPRGPHL VGPSRCLSHL DFVPCPVDTI QIVLPPHLER IREKLAENIH ELWALTRIE QGWTYGPVRD DNKRLHPCLV NFHSLPEPER NYNLQMSGET LKTLLALGCH VGMADEKAED NLKKTKLPKT Y MMSNGYKP APLDLSHVRL TPAQTTLVDR LAENGHNVWA RDRVAQGWSY SAVQDIPARR NPRLVPYRLL DEATKRSNRD SL CQAVRTL LGYGYNIEPP DQEPSQVDSQ SRGDRARIFR AEKSYAVQSG RWYFEFEAVT TGEMRVGWAR PELRPDVELG ADD LAYVFN GHRGQRWHLG SEPFGRPWQS GDVVGCMIDL TENTIIFTLN GEVLMSDSGS ETAFRDIEIG DGFLPVCSLG PGQV GHLNL GQDVSSLRFF AICGLQEGFE PFAINMQRPV TTWFSKSLPQ FEPVPLEHPH YEVARMDGTV DTPPCLRLTH RTWGS QNSL VEMLFLRLSL PVQFHQHFRC TAGATPLASP GLQPPAEDEA RAAEPDTDYE NLRRSAGGWG EAEGGKDGTA KEGTPG GTA QAGVEAQPAR AENEKDATTE KNKKRGFLFK AKKVAMMTQP PSTPALPRLP RDVVPADNRD DPEIILNTTT YYYSVRV FA GQEPSCVWVG WVTPDYHQHD MSFDLSKVRA VTVTMGDEQG NVHSSLKCSN CYMVWGGDFV SPGQQGRISH TDLVIGCL V DLATGLMTFT ANGKESNTFF QVEPNTKLFP AVFVLPTHQN VVQFELGKQK NIMPLSAAMF LSERKNPAPQ CPPRLEVQM LMPVSWSRMP NHFLQVDTRR AGERLGWAVQ CQEPLMMMAL HIPEENRCMD ILELSERLDL QRFHSHTLSL YRSVCALGNN RVAHALCSH VDQAQLLHAL EDARLPGPLR AGYYDLLISI HLESACRSRR SMLSEYIVPL TPETRAITLF PPGRSAEDGP R RHGLPGVG VTTSLRPPHH FSPPCFVVAL PAAGATEAPA RLSPAIPLEA LRDKALRMLG EAVRDGGQHA RDPVGGSVEF QF VPVLKLV STLLVMGVFS DEDVKQILKM IEPEVFREEE EVEEEGEEEE EDEEEKEEDE EEEAHEKEDE EKEEAEDAAE EEK EELEEG LLQMKLPESV KLQMCHLLEY FCDQELQHRV ESLAAFAECY VDKMQGNQRG RYGLLMKAFT MSAAETARRT REFR SPPQE QINMLLHFKN GADEEECPLP EEIRQELVNF HQDLLAHCGI QLEGEEEEPE EESTLGSRLM SLLEKVKLVK KTEEK PEEE PAPEEHKPQS LQELVSHTVV RWAQEDFVQS PELVRAMFSL LHRQYDGLGE LLRALPRAYT ISVSSVEDTM SLLECL GQI RSLLIVQMGP QEENLMIQSI GNIMNNKVFY QHPNLMRALG MHETVMEVMV NVLGGGESKE IRFPKMVTSC CRFLCYF CR ISRQNQRSMF DHLSYLLENS GIGLGMQGST PLDVAAASVI DNNELALALQ EQDLEKVVSY LAGCGLQSCP MLLAKGYP D IGWNPCGGER YLDFLRFAVF VNGESVEENA NVVVRLLIRK PECFGPALRG EGGSGLLAAI EEAIRISEDP ARDGPGVRR DRRREHFGEE PPEENRVHLG HAIMSFYAAL IDLLGRCAPE THLIQAGKGE ALRIRAILRS LVPLDDLVGI ISLPLQIPTL GKDGALVQP KMSASFVPDH KASMVLFLDR VYGIENQDFL LHVLDVGFLP DMRAAASLDT ATFSTTEMAL ALNRYLCLAV L PLITKCAP LFAGTEHRAI MVDSMLHTVY RLSRGRSLTK AQRDVIEDCL MALCRYIRPS MLQHLLRRLV FDVPILNEFA KM PLKLLTN HYERCWKYYC LPTGWANFGV TSEEELHLTR KLFWGIFDSL AHKKYDQELY RIAMPCLCAI AGALPPDYVD ASY SSKTEK KATVDAEGNF DPRPVETLNV IIPEKLDSFI NKFAEYTHEK WAFDKIQNNW SYGENIDEEL KTHPMLRPYK TFSE KDKEI YRWPIKESLK AMIAWEWTVE KAREGEEEKT EKKKTRKISQ TAQTYDPREG YNPQPPDLSV VTLSRELQAM AEQLA ENYH NTWGRKKKQE LEAKGGGSHP LLVPYDTLTA KEKARDREKA QELLKFLQMN GYAVTRGLKD MELDTSSIEK RFAFGF LQQ LLRWMDISQE FIAHLEAVVS SGRVEKSPHE QEIKFFAKIL LPLINQYFTN HCLYFLSTPA KVLGSGGHAS NKEKEMI TS LFCKLAALVR HRVSLFGTDA PAVVNCLHIL ARSLDARTVM KSGPEIVKAG LRSFFESASE DIEKMVENLR LGKVSQAR T QVKGVGQNLT YTTVALLPVL TTLFQHIAQH QFGDDVILDD VQVSCYRTLC SIYSLGTTRN PYVEKLRPAL GECLARLAA AMPVAFLEPE LNEYNACSVY TTKSPRERAI LGLPNSVEEM CPDIPVLERL MAEIGGLAES GARYTEMPHV IEITLPMLCS YLPRWWERG PEAPPPALPA GAPPPCTAVT SDHLNSLLGN ILRIIVNNLG IDEASWMKRL AVFAQPIVSR ARPELLRSHF I PTIGRLRK RAGKVVAEEE QLRLEAKAEA EEGELLVRDE FSVLCRDLYA LYPLLIRYVD NNRAHWLTEP NPNAEELFRM VG EIFIYWS KSHNFKREEQ NFVVQNEINN MSFLTADNKS KMAKAGDVQS GGSDQERTKK KRRGDRYSVQ TSLIVATLKK MLP IGLNMC APTDQDLIVL AKARYALKDT DEEVREFLQN NLNLQGKVEG SPSLRWQMAL YRGVPGREED ADDPEKIVRR VQEV SAVLY HLDQTEHPYK SKKAVWHKLL SKQRRRAVVA CFRMTPLYNL PTHRACNMFL ESYKASWILT EDHSFEDRMI DDLSK AGEQ EEEEEEVEEK KPDPLHQLVL HFSRTALTEK SKLDEDYLYM AYADIMAKSC HLEEGGENGE EGGEEEEVEV SFEEKE MEK QRLLYQQSRL HNRGAAEMVL QMISACKGET GAMVSSTLKL GISILNGGNA EVQQKMLDYL KDKKEVGFFQ SIQALMQ TC SVLDLNAFER QNKAEGLGMV NEDGTVINRQ NGEKVMADDE FTQDLFRFLQ LLCEGHNNDF QNYLRTQTGN TTTINIII C TVDYLLRLQE SISDFYWYYS GKDVIEEQGK RNFSKAMSVA KQVFNSLTEY IQGPCTGNQQ SLAHSRLWDA VVGFLHVFA HMMMKLAQDS SQIELLKELL DLQKDMVVML LSLLEGNVVN GMIARQMVDM LVESSSNVEM ILKFFDMFLK LKDIVGSEAF QDYVTDPRG LISKKDFQKA MDSQKQFTGP EIQFLLSCSE ADENEMINCE EFANRFQEPA RDIGFNVAVL LTNLSEHVPH D PRLRNFLE LAESILEYFR PYLGRIEIMG ASRRIERIYF EISETNRAQW EMPQVKESKR QFIFDVVNEG GESEKMEMFV SF CEDTIFE MQIAAQISEP EGEPEEDEDE GAEEAEEGAA GSDGSGSAAA AGVWVWLAAT AGRTLRGLSY RSLRRRVRRL RRL TAREAA TAVAALLWAL VTRAGGAGAG AAAGALRLLW GSLFGGGLVD SAKKVTVTEL LAGMPDPTGD EVHGQQPSGA GSDA EGEGE GEGEGDAADG AGDEEAAADQ AGTGGADGAV AVADGSPFRP EGAGGLGDMG DTTPVEPPTP EGSPILKRKL GVDGE EEEP PPEPEPEPEP EPEKADTENG EKEVPEPPPE PPKKTPPPPP PKKEEAGGAG LEEFWGELEV QRVKFLNYLS RNFYTL RFL ALFLAFAINF ILLFYKVSDS PPGEDDIEGS GAGDMSGAGS GDGSGWGSRA GEEVEGDEDE NMVYYFLEES TGYMEPA LR CLSLLHTLVA FLCIIGYNCL KVPLVIFKRE KELARKLEFD GLYITEQPED DDVKGQWDRL VLNTPSFPSN YWDKFVKR K VLDKHGDIFG RERIAELLGM DLASLEITAH NERKPDPPPG LLTWIMSIDV KYQIWKFGVI FTDNSFLYLG WYMVMSLLG HYNNFFFAAH LLDIAMGVKT LRTILSSVTH NGKQLVMTVG LLAVVVYLYT VVAFNFFRKF YNKSEDEDEP DMKCDDMMTC YLFHMYVGV RAGGGIGDEI EDPAGDEYEL YRVVFDITFF FFVIVILLAI IQGLIIDAFG ELRDQQEQVK EDMETKCFIC G IGSDYFDT TPHGFETHTL EEHNLANYMF FLMYLINKDE TEHTGQESYV WKMYQERCWD FFPAGDCFRK QYEDQLS UniProtKB: Ryanodine receptor 1 |
-Macromolecule #4: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 20 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #6: CAFFEINE
Macromolecule | Name: CAFFEINE / type: ligand / ID: 6 / Number of copies: 4 / Formula: CFF |
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Molecular weight | Theoretical: 194.191 Da |
Chemical component information | ![]() ChemComp-CFF: |
-Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 8 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Macromolecule #8: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 8 / Number of copies: 8 / Formula: PCW |
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Molecular weight | Theoretical: 787.121 Da |
Chemical component information | ![]() ChemComp-PCW: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 8.5 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV | |||||||||||||||||||||
Details | 0.15 mmol/L S100A1-dimer |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 12555 / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen 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
Startup model | Type of model: INSILICO MODEL / In silico model: CryoSPARC ab initio |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 31572 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: CryoSPARC branch-and-bound |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: CryoSPARC branch-and-bound |