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- EMDB-42461: Structure of human RyR2-S2808D in the primed state in the presenc... -

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Basic information

Entry
Database: EMDB / ID: EMD-42461
TitleStructure of human RyR2-S2808D in the primed state in the presence of Rapamycin
Map dataComposite map of the Structure of human RyR2-S2808D in the primed state in the presence of Rapamycin
Sample
  • Complex: Complex of RyR2-S2808D
    • Protein or peptide: Ryanodine receptor 2
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordscalcium channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


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 / positive regulation of ATPase-coupled calcium transmembrane transporter 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 / positive regulation of ATPase-coupled calcium transmembrane transporter activity / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / embryonic heart tube morphogenesis / regulation of cardiac muscle contraction by calcium ion signaling / cardiac muscle hypertrophy / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to muscle activity / calcium ion transport into cytosol / response to caffeine / cell communication by electrical coupling involved in cardiac conduction / response to redox state / positive regulation of heart rate / cellular response to caffeine / protein kinase A regulatory subunit binding / smooth endoplasmic reticulum / intracellularly gated calcium channel activity / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / : / detection of calcium ion / striated muscle contraction / regulation of cardiac muscle contraction / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / release of sequestered calcium ion into cytosol / Ion homeostasis / cardiac muscle contraction / cellular response to epinephrine stimulus / sarcoplasmic reticulum membrane / calcium channel complex / regulation of cytosolic calcium ion concentration / response to muscle stretch / regulation of heart rate / sarcoplasmic reticulum / establishment of localization in cell / calcium-mediated signaling / sarcolemma / calcium channel activity / Stimuli-sensing channels / intracellular calcium ion homeostasis / Z disc / : / calcium ion transport / transmembrane transporter binding / response to hypoxia / calmodulin binding / calcium ion binding / enzyme binding / protein-containing complex / membrane / identical protein binding / plasma membrane
Similarity search - Function
: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / 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 junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / 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 / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / EF-hand domain pair / Ion transport domain / Ion transport protein / EF-hand domain / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.96 Å
AuthorsMiotto MC / Marks AR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL145473 United States
CitationJournal: To Be Published
Title: Structural basis for ryanodine receptor type 2 leak in heart failure and arrhythmogenic disorders
Authors: Miotto MC
History
DepositionOct 23, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateNov 15, 2023-
Current statusNov 15, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42461.png

Downloads & links

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Map

FileDownload / File: emd_42461.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the Structure of human RyR2-S2808D in the primed state in the presence of Rapamycin
Voxel sizeX=Y=Z: 0.83 Å
Density
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.016484555 - 0.47317
Average (Standard dev.)0.008358672 (±0.022489134)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 424.96 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Raw consensus map of the Structure of human...

Fileemd_42461_additional_1.map
AnnotationRaw consensus map of the Structure of human RyR2-S2808D in the primed state in the presence of Rapamycin
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 of RyR2-S2808D

EntireName: Complex of RyR2-S2808D
Components
  • Complex: Complex of RyR2-S2808D
    • Protein or peptide: Ryanodine receptor 2
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Complex of RyR2-S2808D

SupramoleculeName: Complex of RyR2-S2808D / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ryanodine receptor 2

MacromoleculeName: Ryanodine receptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 565.314125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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 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 RIDQTSQVSV 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

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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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

Concentration2.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
230.0 mMNaClSodium chloridesodium chloride
10.0 mMHEPESHEPES
0.4 %CHAPSCHAPS
1.0 mMEGTAEGTA
0.5 mMTCEPtris(2-carboxyethyl)phosphine
0.001 %DOPCDOPC
10.0 mMATPAdenosine triphosphateATPAdenosine triphosphate
0.25 mMRapamycinSirolimusrapamycinSirolimus

Details: 30-minute incubation with rapamycin was stopped by flash freezing (vitrobot)
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 80.0 K / Max: 100.0 K
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: CryoSPARC ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18232

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Atomic model buiding 1

Initial modelPDB ID:

7ua5


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8uq5:
Structure of human RyR2-S2808D in the primed state in the presence of Rapamycin

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