[English] 日本語
Yorodumi
- EMDB-42762: Structure of PKA phosphorylated human RyR2-R420W in the primed state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-42762
TitleStructure of PKA phosphorylated human RyR2-R420W in the primed state
Map dataComposite map of the Structure of PKA phosphorylated human RyR2-R420W in the primed state
Sample
  • Complex: Complex of RyR2-R420W and Calstabin-2
    • Complex: Ryanodine Receptor 2
      • Protein or peptide: Ryanodine receptor 2
    • Complex: Peptidyl- cis-trans isomerase FKBP1B
      • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordscalcium channel / MEMBRANE PROTEIN
Function / homology
Function and homology information


calcium-induced calcium release activity / junctional sarcoplasmic reticulum membrane / sarcoplasmic reticulum calcium ion transport / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / suramin binding / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis ...calcium-induced calcium release activity / junctional sarcoplasmic reticulum membrane / sarcoplasmic reticulum calcium ion transport / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / suramin binding / 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 / cell communication by electrical coupling involved in cardiac conduction / regulation of ventricular cardiac muscle cell action potential / 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 / cardiac muscle hypertrophy / negative regulation of insulin secretion involved in cellular response to glucose stimulus / regulation of cardiac muscle contraction by calcium ion signaling / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / calcium ion transport into cytosol / ryanodine-sensitive calcium-release channel activity / response to caffeine / response to redox state / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / : / 'de novo' protein folding / negative regulation of heart rate / response to muscle activity / FK506 binding / positive regulation of axon regeneration / channel regulator activity / protein kinase A regulatory subunit binding / protein kinase A catalytic subunit binding / positive regulation of the force of heart contraction / cellular response to caffeine / intracellularly gated calcium channel activity / smooth muscle contraction / regulation of cardiac muscle contraction / detection of calcium ion / response to vitamin E / regulation of cytosolic calcium ion concentration / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / smooth endoplasmic reticulum / regulation of ryanodine-sensitive calcium-release channel activity / striated muscle contraction / positive regulation of heart rate / T cell proliferation / cardiac muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / release of sequestered calcium ion into cytosol / calcium channel complex / cellular response to epinephrine stimulus / response to muscle stretch / sarcoplasmic reticulum membrane / regulation of heart rate / sarcoplasmic reticulum / establishment of localization in cell / peptidyl-prolyl cis-trans isomerase activity / peptidylprolyl isomerase / calcium-mediated signaling / sarcolemma / calcium channel activity / response to hydrogen peroxide / Stimuli-sensing channels / 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 / cytoplasm
Similarity search - Function
Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / 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. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / EF-hand domain pair / EF-hand domain / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP1B / Ryanodine receptor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.13 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: Nat Commun / Year: 2024
Title: Structural basis for ryanodine receptor type 2 leak in heart failure and arrhythmogenic disorders.
Authors: Marco C Miotto / Steven Reiken / Anetta Wronska / Qi Yuan / Haikel Dridi / Yang Liu / Gunnar Weninger / Carl Tchagou / Andrew R Marks /
Abstract: Heart failure, the leading cause of mortality and morbidity in the developed world, is characterized by cardiac ryanodine receptor 2 channels that are hyperphosphorylated, oxidized, and depleted of ...Heart failure, the leading cause of mortality and morbidity in the developed world, is characterized by cardiac ryanodine receptor 2 channels that are hyperphosphorylated, oxidized, and depleted of the stabilizing subunit calstabin-2. This results in a diastolic sarcoplasmic reticulum Ca leak that impairs cardiac contractility and triggers arrhythmias. Genetic mutations in ryanodine receptor 2 can also cause Ca leak, leading to arrhythmias and sudden cardiac death. Here, we solved the cryogenic electron microscopy structures of ryanodine receptor 2 variants linked either to heart failure or inherited sudden cardiac death. All are in the primed state, part way between closed and open. Binding of Rycal drugs to ryanodine receptor 2 channels reverts the primed state back towards the closed state, decreasing Ca leak, improving cardiac function, and preventing arrhythmias. We propose a structural-physiological mechanism whereby the ryanodine receptor 2 channel primed state underlies the arrhythmias in heart failure and arrhythmogenic disorders.
History
DepositionNov 9, 2023-
Header (metadata) releaseNov 22, 2023-
Map releaseNov 22, 2023-
UpdateNov 13, 2024-
Current statusNov 13, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_42762.png

Downloads & links

-
Map

FileDownload / File: emd_42762.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the Structure of PKA phosphorylated human RyR2-R420W in the primed state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 512 pix.
= 430.848 Å		0.84 Å/pix.
x 512 pix.
= 430.848 Å		0.84 Å/pix.
x 512 pix.
= 430.848 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8415 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.12
Minimum - Maximum-0.013472379 - 0.64614874
Average (Standard dev.)0.01058729 (±0.031439014)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 430.848 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Raw consensus map of the Structure of PKA...

Fileemd_42762_additional_1.map
AnnotationRaw consensus map of the Structure of PKA phosphorylated human RyR2-R420W in the primed state
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of RyR2-R420W and Calstabin-2

EntireName: Complex of RyR2-R420W and Calstabin-2
Components
  • Complex: Complex of RyR2-R420W and Calstabin-2
    • Complex: Ryanodine Receptor 2
      • Protein or peptide: Ryanodine receptor 2
    • Complex: Peptidyl- cis-trans isomerase FKBP1B
      • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: Complex of RyR2-R420W and Calstabin-2

SupramoleculeName: Complex of RyR2-R420W and Calstabin-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

-
Supramolecule #2: Ryanodine Receptor 2

SupramoleculeName: Ryanodine Receptor 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

-
Supramolecule #3: Peptidyl- cis-trans isomerase FKBP1B

SupramoleculeName: Peptidyl- cis-trans isomerase FKBP1B / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

-
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: 565.315125 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 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

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.798501 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGVEIETISP GDGRTFPKKG QTCVVHYTGM LQNGKKFDSS RDRNKPFKFR IGKQEVIKGF EEGAAQMSLG QRAKLTCTPD VAYGATGHP GVIPPNATLI FDVELLNLE

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B

-
Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration2.5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
230.0 mMNaClsodium chloride
10.0 mMHEPES
0.4 %CHAPS
1.0 mMEGTA
0.5 mMtris(2-carboxyethyl)phosphine
0.001 %DOPC
10.0 mMATP
VitrificationCryogen name: ETHANE

-
Electron microscopy

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

-
Image processing

Startup modelType of model: INSILICO MODEL / In silico model: CryoSPARC ab initio
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 102478
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
Atomic model buiding 1

Initial modelPDB ID:

7ua5


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

PDB-8uxf:
Structure of PKA phosphorylated human RyR2-R420W in the primed state

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more