+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-43283 | |||||||||
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Title | Structure of mouse RyR1 (EGTA-only dataset) | |||||||||
Map data | mouse RyR1 (EGTA-only dataset) | |||||||||
Sample |
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Keywords | Calcium / Ion Channel / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information junctional membrane complex / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / mTORC1-mediated signalling / activin receptor binding / cytoplasmic side of membrane / regulation of muscle contraction / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / regulation of response to osmotic stress ...junctional membrane complex / TGF-beta receptor signaling activates SMADs / Calcineurin activates NFAT / mTORC1-mediated signalling / activin receptor binding / cytoplasmic side of membrane / regulation of muscle contraction / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / regulation of response to osmotic stress / transforming growth factor beta receptor binding / signaling receptor inhibitor activity / Stimuli-sensing channels / type I transforming growth factor beta receptor binding / Ion homeostasis / heart trabecula formation / terminal cisterna / ryanodine receptor complex / I-SMAD binding / ryanodine-sensitive calcium-release channel activity / I band / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / response to caffeine / skin development / cellular response to ATP / ventricular cardiac muscle tissue morphogenesis / FK506 binding / cellular response to caffeine / outflow tract morphogenesis / smooth endoplasmic reticulum / organelle membrane / striated muscle contraction / voltage-gated calcium channel activity / T cell proliferation / skeletal muscle fiber development / axon terminus / heart morphogenesis / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / Hsp70 protein binding / sarcoplasmic reticulum membrane / T-tubule / calcium channel complex / regulation of cytosolic calcium ion concentration / cellular response to calcium ion / extrinsic component of cytoplasmic side of plasma membrane / sarcomere / sarcoplasmic reticulum / muscle contraction / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / negative regulation of transforming growth factor beta receptor signaling pathway / sarcolemma / calcium channel activity / cytoplasmic side of plasma membrane / Z disc / cytokine-mediated signaling pathway / calcium ion transport / cell cortex / protein homotetramerization / protease binding / vesicle / transmembrane transporter binding / response to hypoxia / calmodulin binding / synapse / calcium ion binding / perinuclear region of cytoplasm / enzyme binding / protein-containing complex / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.53 Å | |||||||||
Authors | Weninger G / Marks AR | |||||||||
Funding support | United States, 1 items
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Citation | Journal: To Be Published Title: Structural insights into the regulation of RyR1 by S100A1. Authors: Weninger G | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_43283.map.gz | 34.6 MB | EMDB map data format | |
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Header (meta data) | emd-43283-v30.xml emd-43283.xml | 24 KB 24 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_43283_fsc.xml | 16.9 KB | Display | FSC data file |
Images | emd_43283.png | 76.4 KB | ||
Filedesc metadata | emd-43283.cif.gz | 8.9 KB | ||
Others | emd_43283_half_map_1.map.gz emd_43283_half_map_2.map.gz | 475 MB 475 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-43283 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-43283 | HTTPS FTP |
-Related structure data
Related structure data | 8vjjMC 8vjkC 8vk4C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_43283.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | mouse RyR1 (EGTA-only dataset) | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.837 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_43283_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_43283_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of RyR1 with Calstabin-1 (EGTA condition)
Entire | Name: Complex of RyR1 with Calstabin-1 (EGTA condition) |
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Components |
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-Supramolecule #1: Complex of RyR1 with Calstabin-1 (EGTA condition)
Supramolecule | Name: Complex of RyR1 with Calstabin-1 (EGTA condition) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-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: Mus musculus (house mouse) |
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 #2: Peptidyl-prolyl cis-trans isomerase FKBP1A
Macromolecule | Name: Peptidyl-prolyl cis-trans isomerase FKBP1A / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase |
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Source (natural) | Organism: Mus musculus (house mouse) |
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 #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #4: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
Macromolecule | Name: 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / type: ligand / ID: 4 / 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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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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 |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 12147 / Average electron dose: 58.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |