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- EMDB-26409: Structure of PKA phosphorylated human RyR2-R2474S in the closed state -
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Open data
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Basic information
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Title | Structure of PKA phosphorylated human RyR2-R2474S in the closed state | |||||||||
![]() | Composite map of the Structure of PKA phosphorylated human RyR2-R2474S in the closed state. | |||||||||
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Function / homology | ![]() junctional sarcoplasmic reticulum membrane / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / regulation of AV node cell action potential / calcium-induced calcium release activity ...junctional sarcoplasmic reticulum membrane / suramin binding / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / regulation of AV node cell action potential / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / cell communication by electrical coupling involved in cardiac conduction / ventricular cardiac muscle cell action potential / regulation of ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / embryonic heart tube morphogenesis / negative regulation of insulin secretion involved in cellular response to glucose stimulus / cardiac muscle hypertrophy / negative regulation of release of sequestered calcium ion into cytosol / ryanodine-sensitive calcium-release channel activity / regulation of cardiac muscle contraction by calcium ion signaling / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to muscle activity / calcium ion transport into cytosol / response to caffeine / response to redox state / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / positive regulation of heart rate / FK506 binding / positive regulation of axon regeneration / cellular response to caffeine / protein kinase A regulatory subunit binding / channel regulator activity / intracellularly gated calcium channel activity / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / detection of calcium ion / smooth muscle contraction / regulation of cardiac muscle contraction / smooth endoplasmic reticulum / response to vitamin E / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / T cell proliferation / cardiac muscle contraction / release of sequestered calcium ion into cytosol / Ion homeostasis / regulation of cytosolic calcium ion concentration / sarcoplasmic reticulum membrane / calcium channel complex / cellular response to epinephrine stimulus / response to muscle stretch / regulation of heart rate / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / establishment of localization in cell / calcium-mediated signaling / response to hydrogen peroxide / calcium channel activity / Stimuli-sensing channels / sarcolemma / Z disc / intracellular calcium ion homeostasis / calcium ion transport / positive regulation of cytosolic calcium ion concentration / protein refolding / transmembrane transporter binding / response to hypoxia / calmodulin binding / signaling receptor binding / calcium ion binding / enzyme binding / protein-containing complex / identical protein binding / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.58 Å | |||||||||
![]() | Miotto MC / Marks AR | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural analyses of human ryanodine receptor type 2 channels reveal the mechanisms for sudden cardiac death and treatment. Authors: Marco C Miotto / Gunnar Weninger / Haikel Dridi / Qi Yuan / Yang Liu / Anetta Wronska / Zephan Melville / Leah Sittenfeld / Steven Reiken / Andrew R Marks / ![]() Abstract: Ryanodine receptor type 2 (RyR2) mutations have been linked to an inherited form of exercise-induced sudden cardiac death called catecholaminergic polymorphic ventricular tachycardia (CPVT). CPVT ...Ryanodine receptor type 2 (RyR2) mutations have been linked to an inherited form of exercise-induced sudden cardiac death called catecholaminergic polymorphic ventricular tachycardia (CPVT). CPVT results from stress-induced sarcoplasmic reticular Ca leak via the mutant RyR2 channels during diastole. We present atomic models of human wild-type (WT) RyR2 and the CPVT mutant RyR2-R2474S determined by cryo-electron microscopy with overall resolutions in the range of 2.6 to 3.6 Å, and reaching local resolutions of 2.25 Å, unprecedented for RyR2 channels. Under nonactivating conditions, the RyR2-R2474S channel is in a "primed" state between the closed and open states of WT RyR2, rendering it more sensitive to activation that results in stress-induced Ca leak. The Rycal drug ARM210 binds to RyR2-R2474S, reverting the primed state toward the closed state. Together, these studies provide a mechanism for CPVT and for the therapeutic actions of ARM210. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 248 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.8 KB 20.8 KB | Display Display | ![]() |
Images | ![]() | 136.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7u9xMC ![]() 7u9qC ![]() 7u9rC ![]() 7u9tC ![]() 7u9zC ![]() 7ua1C ![]() 7ua3C ![]() 7ua4C ![]() 7ua5C ![]() 7ua9C M: atomic model generated by this map C: citing same article ( |
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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 | Composite map of the Structure of PKA phosphorylated human RyR2-R2474S in the closed state. | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 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 RyR2-R2474S and Calstabin-2
Entire | Name: Complex of RyR2-R2474S and Calstabin-2 |
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Components |
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-Supramolecule #1: Complex of RyR2-R2474S and Calstabin-2
Supramolecule | Name: Complex of RyR2-R2474S and Calstabin-2 / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: Ryanodine receptor 2
Supramolecule | Name: Ryanodine receptor 2 / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() |
-Supramolecule #3: Peptidyl- cis-trans isomerase FKBP1B
Supramolecule | Name: Peptidyl- cis-trans isomerase FKBP1B / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #1: Ryanodine receptor 2
Macromolecule | Name: Ryanodine receptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 565.216 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MADGGEGEDE IQFLRTDDEV VLQCTATIHK EQQKLCLAAE GFGNRLCFLE STSNSKNVPP DLSICTFVLE QSLSVRALQE MLANTVEKS EGQVDVEKWK FMMKTAQGGG HRTLLYGHAI LLRHSYSGMY LCCLSTSRSS TDKLAFDVGL QEDTTGEACW W TIHPASKQ ...String: MADGGEGEDE IQFLRTDDEV VLQCTATIHK EQQKLCLAAE GFGNRLCFLE STSNSKNVPP DLSICTFVLE QSLSVRALQE MLANTVEKS EGQVDVEKWK FMMKTAQGGG HRTLLYGHAI LLRHSYSGMY LCCLSTSRSS TDKLAFDVGL QEDTTGEACW W TIHPASKQ RSEGEKVRVG DDLILVSVSS ERYLHLSYGN GSLHVDAAFQ QTLWSVAPIS SGSEAAQGYL IGGDVLRLLH GH MDECLTV PSGEHGEEQR RTVHYEGGAV SVHARSLWRL ETLRVAWSGS HIRWGQPFRL RHVTTGKYLS LMEDKNLLLM DKE KADVKS TAFTFRSSKE KLDVGVRKEV DGMGTSEIKY GDSVCYIQHV DTGLWLTYQS VDVKSVRMGS IQRKAIMHHE GHMD DGISL SRSQHEESRT ARVIRSTVFL FNRFIRGLDA LSKKAKASTV DLPIESVSLS LQDLIGYFHP PDEHLEHEDK QNRLR ALKN RQNLFQEEGM INLVLECIDR LHVYSSAAHF ADVAGREAGE SWKSILNSLY ELLAALIRGN RKNCAQFSGS LDWLIS RLE RLEASSGILE VLHCVLVESP EALNIIKEGH IKSIISLLDK HGRNHKVLDV LCSLCVCHGV AVRSNQHLIC DNLLPGR DL LLQTRLVNHV SSMRPNIFLG VSEGSAQYKK WYYELMVDHT EPFVTAEATH LRVGWASTEG YSPYPGGGEE WGGNGVGD D LFSYGFDGLH LWSGCIARTV SSPNQHLLRT DDVISCCLDL SAPSISFRIN GQPVQGMFEN FNIDGLFFPV VSFSAGIKV RFLLGGRHGE FKFLPPPGYA PCYEAVLPKE KLKVEHSREY KQERTYTRDL LGPTVSLTQA AFTPIPVDTS QIVLPPHLER IREKLAENI HELWVMNKIE LGWQYGPVRD DNKRQHPCLV EFSKLPEQER NYNLQMSLET LKTLLALGCH VGISDEHAED K VKKMKLPK NYQLTSGYKP APMDLSFIKL TPSQEAMVDK LAENAHNVWA RDRIRQGWTY GIQQDVKNRR NPRLVPYTLL DD RTKKSNK DSLREAVRTL LGYGYNLEAP DQDHAARAEV CSGTGERFRI FRAEKTYAVK AGRWYFEFET VTAGDMRVGW SRP GCQPDQ ELGSDERAFA FDGFKAQRWH QGNEHYGRSW QAGDVVGCMV DMNEHTMMFT LNGEILLDDS GSELAFKDFD VGDG FIPVC SLGVAQVGRM NFGKDVSTLK YFTICGLQEG YEPFAVNTNR DITMWLSKRL PQFLQVPSNH EHIEVTRIDG TIDSS PCLK VTQKSFGSQN SNTDIMFYRL SMPIECAEVF SKTVAGGLPG AGLFGPKNDL EDYDADSDFE VLMKTAHGHL VPDRVD KDK EATKPEFNNH KDYAQEKPSR LKQRFLLRRT KPDYSTSHSA RLTEDVLADD RDDYDFLMQT STYYYSVRIF PGQEPAN VW VGWITSDFHQ YDTGFDLDRV RTVTVTLGDE KGKVHESIKR SNCYMVCAGE SMSPGQGRNN NGLEIGCVVD AASGLLTF I ANGKELSTYY QVEPSTKLFP AVFAQATSPN VFQFELGRIK NVMPLSAGLF KSEHKNPVPQ CPPRLHVQFL SHVLWSRMP NQFLKVDVSR ISERQGWLVQ CLDPLQFMSL HIPEENRSVD ILELTEQEEL LKFHYHTLRL YSAVCALGNH RVAHALCSHV DEPQLLYAI ENKYMPGLLR AGYYDLLIDI HLSSYATARL MMNNEYIVPM TEETKSITLF PDENKKHGLP GIGLSTSLRP R MQFSSPSF VSISNECYQY SPEFPLDILK SKTIQMLTEA VKEGSLHARD PVGGTTEFLF VPLIKLFYTL LIMGIFHNED LK HILQLIE PSVFKEAATP EEESDTLEKE LSVDDAKLQG AGEEEAKGGK RPKEGLLQMK LPEPVKLQMC LLLQYLCDCQ VRH RIEAIV AFSDDFVAKL QDNQRFRYNE VMQALNMSAA LTARKTKEFR SPPQEQINML LNFKDDKSEC PCPEEIRDQL LDFH EDLMT HCGIELDEDG SLDGNSDLTI RGRLLSLVEK VTYLKKKQAE KPVESDSKKS STLQQLISET MVRWAQESVI EDPEL VRAM FVLLHRQYDG IGGLVRALPK TYTINGVSVE DTINLLASLG QIRSLLSVRM GKEEEKLMIR GLGDIMNNKV FYQHPN LMR ALGMHETVME VMVNVLGGGE SKEITFPKMV ANCCRFLCYF CRISRQNQKA MFDHLSYLLE NSSVGLASPA MRGSTPL DV AAASVMDNNE LALALREPDL EKVVRYLAGC GLQSCQMLVS KGYPDIGWNP VEGERYLDFL RFAVFCNGES VEENANVV V RLLIRRPECF GPALRGEGGN GLLAAMEEAI KIAEDPSRDG PSPNSGSSKT LDTEEEEDDT IHMGNAIMTF YSALIDLLG RCAPEMHLIH AGKGEAIRIR SILRSLIPLG DLVGVISIAF QMPTIAKDGN VVEPDMSAGF CPDHKAAMVL FLDSVYGIEV QDFLLHLLE VGFLPDLRAA ASLDTAALSA TDMALALNRY LCTAVLPLLT RCAPLFAGTE HHASLIDSLL HTVYRLSKGC S LTKAQRDS IEVCLLSICG QLRPSMMQHL LRRLVFDVPL LNEHAKMPLK LLTNHYERCW KYYCLPGGWG NFGAASEEEL HL SRKLFWG IFDALSQKKY EQELFKLALP CLSAVAGALP PDYMESNYVS MMEKQSSMDS EGNFNPQPVD TSNITIPEKL EYF INKYAE HSHDKWSMDK LANGWIYGEI YSDSSKVQPL MKPYKLLSEK EKEIYRWPIK ESLKTMLAWG WRIERTREGD SMAL YNRTR RISQTSQVSV DAAHGYSPRA IDMSNVTLSR DLHAMAEMMA ENYHNIWAKK KKMELESKGG GNHPLLVPYD TLTAK EKAK DREKAQDILK FLQINGYAVS RGFKDLELDT PSIEKRFAYS FLQQLIRYVD EAHQYILEFD GGSRGKGEHF PYEQEI KFF AKVVLPLIDQ YFKNHRLYFL SAASRPLCSG GHASNKEKEM VTSLFCKLGV LVRHRISLFG NDATSIVNCL HILGQTL DA RTVMKTGLES VKSALRAFLD NAAEDLEKTM ENLKQGQFTH TRNQPKGVTQ IINYTTVALL PMLSSLFEHI GQHQFGED L ILEDVQVSCY RILTSLYALG TSKSIYVERQ RSALGECLAA FAGAFPVAFL ETHLDKHNIY SIYNTKSSRE RAALSLPTN VEDVCPNIPS LEKLMEEIVE LAESGIRYTQ MPHVMEVILP MLCSYMSRWW EHGPENNPER AEMCCTALNS EHMNTLLGNI LKIIYNNLG IDEGAWMKRL AVFSQPIINK VKPQLLKTHF LPLMEKLKKK AATVVSEEDH LKAEARGDMS EAELLILDEF T TLARDLYA FYPLLIRFVD YNRAKWLKEP NPEAEELFRM VAEVFIYWSK SHNFKREEQN FVVQNEINNM SFLITDTKSK MS KAAVSDQ ERKKMKRKGD RYSMQTSLIV AALKRLLPIG LNICAPGDQE LIALAKNRFS LKDTEDEVRD IIRSNIHLQG KLE DPAIRW QMALYKDLPN RTDDTSDPEK TVERVLDIAN VLFHLEQKSK RVGRRHYCLV EHPQRSKKAV WHKLLSKQRK RAVV ACFRM APLYNLPRHR AVNLFLQGYE KSWIETEEHY FEDKLIEDLA KPGAEPPEED EGTKRVDPLH QLILLFSRTA LTEKC KLEE DFLYMAYADI MAKSCHDEED DDGEEEVKSF EEKEMEKQKL LYQQARLHDR GAAEMVLQTI SASKGETGPM VAATLK LGI AILNGGNSTV QQKMLDYLKE KKDVGFFQSL AGLMQSCSVL DLNAFERQNK AEGLGMVTEE GSGEKVLQDD EFTCDLF RF LQLLCEGHNS DFQNYLRTQT GNNTTVNIII STVDYLLRVQ ESISDFYWYY SGKDVIDEQG QRNFSKAIQV AKQVFNTL T EYIQGPCTGN QQSLAHSRLW DAVVGFLHVF AHMQMKLSQD SSQIELLKEL MDLQKDMVVM LLSMLEGNVV NGTIGKQMV DMLVESSNNV EMILKFFDMF LKLKDLTSSD TFKEYDPDGK GVISKRDFHK AMESHKHYTQ SETEFLLSCA ETDENETLDY EEFVKRFHE PAKDIGFNVA VLLTNLSEHM PNDTRLQTFL ELAESVLNYF QPFLGRIEIM GSAKRIERVY FEISESSRTQ W EKPQVKES KRQFIFDVVN EGGEKEKMEL FVNFCEDTIF EMQLAAQISE SDLNERSANK EESEKERPEE QGPRMAFFSI LT VRSALFA LRYNILTLMR MLSLKSLKKQ MKKVKKMTVK DMVTAFFSSY WSIFMTLLHF VASVFRGFFR IICSLLLGGS LVE GAKKIK VAELLANMPD PTQDEVRGDG EEGERKPLEA ALPSEDLTDL KELTEESDLL SDIFGLDLKR EGGQYKLIPH NPNA GLSDL MSNPVPMPEV QEKFQEQKAK EEEKEEKEET KSEPEKAEGE DGEKEEKAKE DKGKQKLRQL HTHRYGEPEV PESAF WKKI IAYQQKLLNY FARNFYNMRM LALFVAFAIN FILLFYKVST SSVVEGKELP TRSSSENAKV TSLDSSSHRI IAVHYV LEE SSGYMEPTLR ILAILHTVIS FFCIIGYYCL KVPLVIFKRE KEVARKLEFD GLYITEQPSE DDIKGQWDRL VINTQSF PN NYWDKFVKRK VMDKYGEFYG RDRISELLGM DKAALDFSDA REKKKPKKDS SLSAVLNSID VKYQMWKLGV VFTDNSFL Y LAWYMTMSVL GHYNNFFFAA HLLDIAMGFK TLRTILSSVT HNGKQLVLTV GLLAVVVYLY TVVAFNFFRK FYNKSEDGD TPDMKCDDML TCYMFHMYVG VRAGGGIGDE IEDPAGDEYE IYRIIFDITF FFFVIVILLA IIQGLIIDAF GELRDQQEQV KEDMETKCF ICGIGNDYFD TVPHGFETHT LQEHNLANYL FFLMYLINKD ETEHTGQESY VWKMYQERCW EFFPAGDCFR K QYEDQLN |
-Macromolecule #2: Peptidyl-prolyl cis-trans isomerase FKBP1B
Macromolecule | Name: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.798501 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGVEIETISP GDGRTFPKKG QTCVVHYTGM LQNGKKFDSS RDRNKPFKFR IGKQEVIKGF EEGAAQMSLG QRAKLTCTPD VAYGATGHP GVIPPNATLI FDVELLNLE |
-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: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 8 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.2 mg/mL | |||||||||||||||||||||||||||||||||
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Buffer | pH: 7.4 Component:
Details: Xanthine was made fresh to avoid aggregation. Xanthine stock solution was 10 mM in NaOH 0.5 N. | |||||||||||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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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) / Average electron dose: 58.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |