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- EMDB-42763: Structure of PKA phosphorylated human RyR2-R420W in the closed st... -
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Open data
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Basic information
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Title | Structure of PKA phosphorylated human RyR2-R420W in the closed state in the presence of ARM210 | |||||||||
![]() | Composite map of the Structure of PKA phosphorylated human RyR2-R420W in the closed state in the presence of ARM210 | |||||||||
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![]() | calcium channel / TRANSPORT PROTEIN | |||||||||
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: 3.08 Å | |||||||||
![]() | Miotto MC / Marks AR | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis for ryanodine receptor type 2 leak in heart failure and arrhythmogenic disorders Authors: Miotto MC | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 253.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 23.9 KB 23.9 KB | Display Display | ![]() |
Images | ![]() | 215 KB | ||
Filedesc metadata | ![]() | 9.5 KB | ||
Others | ![]() | 251.6 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8uxgMC ![]() 8uq2C ![]() 8uq3C ![]() 8uq4C ![]() 8uq5C ![]() 8uxcC ![]() 8uxeC ![]() 8uxfC ![]() 8uxhC ![]() 8uxiC ![]() 8uxlC ![]() 8uxmC 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 | Composite map of the Structure of PKA phosphorylated human RyR2-R420W in the closed state in the presence of ARM210 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.841 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Raw consensus map of the Structure of PKA...
File | emd_42763_additional_1.map | ||||||||||||
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Annotation | Raw consensus map of the Structure of PKA phosphorylated human RyR2-R420W in the closed state in the presence of ARM210 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex of RyR2-R420W and Calstabin-2
Entire | Name: Complex of RyR2-R420W and Calstabin-2 |
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Components |
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-Supramolecule #1: Complex of RyR2-R420W and Calstabin-2
Supramolecule | Name: Complex of RyR2-R420W and Calstabin-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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-Supramolecule #2: Ryanodine Receptor 2
Supramolecule | Name: Ryanodine Receptor 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Supramolecule #3: Peptidyl- cis-trans isomerase FKBP1B
Supramolecule | Name: Peptidyl- cis-trans isomerase FKBP1B / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | 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: 565.315125 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 ARVIWSTVFL 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 FLDRVYGIEV 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 UniProtKB: Ryanodine receptor 2 |
-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 UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B |
-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: |
-Macromolecule #5: 4-[(7-methoxy-2,3-dihydro-1,4-benzothiazepin-4(5H)-yl)methyl]benz...
Macromolecule | Name: 4-[(7-methoxy-2,3-dihydro-1,4-benzothiazepin-4(5H)-yl)methyl]benzoic acid type: ligand / ID: 5 / Number of copies: 4 / Formula: KVR |
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Molecular weight | Theoretical: 329.413 Da |
Chemical component information | ![]() ChemComp-KVR: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.5 mg/mL | |||||||||||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 80.0 K / Max: 100.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / 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 | Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 181724 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |