[English] 日本語
Yorodumi
- EMDB-26139: Structure of human RyR2 in the closed state. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-26139
TitleStructure of human RyR2 in the closed state.
Map dataStructure of human RyR2 in the closed state
Sample
  • Complex: Complex of RyR2 with Calstabin
    • Protein or peptide: Ryanodine Receptor 2
Keywordscalcium channel / ATP / closed state / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.53 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) United States
CitationJournal: Sci Adv / Year: 2022
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
DepositionFeb 4, 2022-
Header (metadata) releaseAug 24, 2022-
Map releaseAug 24, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_26139.png

Downloads & links

-
Map

FileDownload / File: emd_26139.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of human RyR2 in the closed state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 426.24 Å		0.83 Å/pix.
x 512 pix.
= 426.24 Å		0.83 Å/pix.
x 512 pix.
= 426.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8325 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.381
Minimum - Maximum-0.025854405 - 1.2424275
Average (Standard dev.)0.030909559 (±0.07760225)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.24 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Complex of RyR2 with Calstabin

EntireName: Complex of RyR2 with Calstabin
Components
  • Complex: Complex of RyR2 with Calstabin
    • Protein or peptide: Ryanodine Receptor 2

-
Supramolecule #1: Complex of RyR2 with Calstabin

SupramoleculeName: Complex of RyR2 with Calstabin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Ryanodine Receptor 2

MacromoleculeName: Ryanodine Receptor 2 / type: protein_or_peptide / ID: 1 / Enantiomer: DEXTRO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADGGEGEDE IQFLRTDDEV VLQCTATIHK EQQKLCLAAE GFGNRLCFLE STSNSKNVPP DLSICTFVL EQSLSVRALQ EMLANTVEKS EGQVDVEKWK FMMKTAQGGG HRTLLYGHAI L LRHSYSGM YLCCLSTSRS STDKLAFDVG LQEDTTGEAC WWTIHPASKQ ...String:
MADGGEGEDE IQFLRTDDEV VLQCTATIHK EQQKLCLAAE GFGNRLCFLE STSNSKNVPP DLSICTFVL EQSLSVRALQ EMLANTVEKS EGQVDVEKWK FMMKTAQGGG HRTLLYGHAI L LRHSYSGM YLCCLSTSRS STDKLAFDVG LQEDTTGEAC WWTIHPASKQ RSEGEKVRVG DD LILVSVS SERYLHLSYG NGSLHVDAAF QQTLWSVAPI SSGSEAAQGY LIGGDVLRLL HGH MDECLT VPSGEHGEEQ RRTVHYEGGA VSVHARSLWR LETLRVAWSG SHIRWGQPFR LRHV TTGKY LSLMEDKNLL LMDKEKADVK STAFTFRSSK EKLDVGVRKE VDGMGTSEIK YGDSV CYIQ HVDTGLWLTY QSVDVKSVRM GSIQRKAIMH HEGHMDDGIS LSRSQHEESR TARVIR STV FLFNRFIRGL DALSKKAKAS TVDLPIESVS LSLQDLIGYF HPPDEHLEHE DKQNRLR AL KNRQNLFQEE GMINLVLECI DRLHVYSSAA HFADVAGREA GESWKSILNS LYELLAAL I RGNRKNCAQF SGSLDWLISR LERLEASSGI LEVLHCVLVE SPEALNIIKE GHIKSIISL LDKHGRNHKV LDVLCSLCVC HGVAVRSNQH LICDNLLPGR DLLLQTRLVN HVSSMRPNIF LGVSEGSAQ YKKWYYELMV DHTEPFVTAE ATHLRVGWAS TEGYSPYPGG GEEWGGNGVG D DLFSYGFD GLHLWSGCIA RTVSSPNQHL LRTDDVISCC LDLSAPSISF RINGQPVQGM FE NFNIDGL FFPVVSFSAG IKVRFLLGGR HGEFKFLPPP GYAPCYEAVL PKEKLKVEHS REY KQERTY TRDLLGPTVS LTQAAFTPIP VDTSQIVLPP HLERIREKLA ENIHELWVMN KIEL GWQYG PVRDDNKRQH PCLVEFSKLP EQERNYNLQM SLETLKTLLA LGCHVGISDE HAEDK VKKM KLPKNYQLTS GYKPAPMDLS FIKLTPSQEA MVDKLAENAH NVWARDRIRQ GWTYGI QQD VKNRRNPRLV PYTLLDDRTK KSNKDSLREA VRTLLGYGYN LEAPDQDHAA RAEVCSG TG ERFRIFRAEK TYAVKAGRWY FEFETVTAGD MRVGWSRPGC QPDQELGSDE RAFAFDGF K AQRWHQGNEH YGRSWQAGDV VGCMVDMNEH TMMFTLNGEI LLDDSGSELA FKDFDVGDG FIPVCSLGVA QVGRMNFGKD VSTLKYFTIC GLQEGYEPFA VNTNRDITMW LSKRLPQFLQ VPSNHEHIE VTRIDGTIDS SPCLKVTQKS FGSQNSNTDI MFYRLSMPIE CAEVFSKTVA G GLPGAGLF GPKNDLEDYD ADSDFEVLMK TAHGHLVPDR VDKDKEATKP EFNNHKDYAQ EK PSRLKQR FLLRRTKPDY STSHSARLTE DVLADDRDDY DFLMQTSTYY YSVRIFPGQE PAN VWVGWI TSDFHQYDTG FDLDRVRTVT VTLGDEKGKV HESIKRSNCY MVCAGESMSP GQGR NNNGL EIGCVVDAAS GLLTFIANGK ELSTYYQVEP STKLFPAVFA QATSPNVFQF ELGRI KNVM PLSAGLFKSE HKNPVPQCPP RLHVQFLSHV LWSRMPNQFL KVDVSRISER QGWLVQ CLD PLQFMSLHIP EENRSVDILE LTEQEELLKF HYHTLRLYSA VCALGNHRVA HALCSHV DE PQLLYAIENK YMPGLLRAGY YDLLIDIHLS SYATARLMMN NEYIVPMTEE TKSITLFP D ENKKHGLPGI GLSTSLRPRM QFSSPSFVSI SNECYQYSPE FPLDILKSKT IQMLTEAVK EGSLHARDPV GGTTEFLFVP LIKLFYTLLI MGIFHNEDLK HILQLIEPSV FKEAATPEEE SDTLEKELS VDDAKLQGAG EEEAKGGKRP KEGLLQMKLP EPVKLQMCLL LQYLCDCQVR H RIEAIVAF SDDFVAKLQD NQRFRYNEVM QALNMSAALT ARKTKEFRSP PQEQINMLLN FK DDKSECP CPEEIRDQLL DFHEDLMTHC GIELDEDGSL DGNSDLTIRG RLLSLVEKVT YLK KKQAEK PVESDSKKSS TLQQLISETM VRWAQESVIE DPELVRAMFV LLHRQYDGIG GLVR ALPKT YTINGVSVED TINLLASLGQ IRSLLSVRMG KEEEKLMIRG LGDIMNNKVF YQHPN LMRA LGMHETVMEV MVNVLGGGES KEITFPKMVA NCCRFLCYFC RISRQNQKAM FDHLSY LLE NSSVGLASPA MRGSTPLDVA AASVMDNNEL ALALREPDLE KVVRYLAGCG LQSCQML VS KGYPDIGWNP VEGERYLDFL RFAVFCNGES VEENANVVVR LLIRRPECFG PALRGEGG N GLLAAMEEAI KIAEDPSRDG PSPNSGSSKT LDTEEEEDDT IHMGNAIMTF YSALIDLLG RCAPEMHLIH AGKGEAIRIR SILRSLIPLG DLVGVISIAF QMPTIAKDGN VVEPDMSAGF CPDHKAAMV LFLDRVYGIE VQDFLLHLLE VGFLPDLRAA ASLDTAALSA TDMALALNRY L CTAVLPLL TRCAPLFAGT EHHASLIDSL LHTVYRLSKG CSLTKAQRDS IEVCLLSICG QL RPSMMQH LLRRLVFDVP LLNEHAKMPL KLLTNHYERC WKYYCLPGGW GNFGAASEEE LHL SRKLFW GIFDALSQKK YEQELFKLAL PCLSAVAGAL PPDYMESNYV SMMEKQSSMD SEGN FNPQP VDTSNITIPE KLEYFINKYA EHSHDKWSMD KLANGWIYGE IYSDSSKVQP LMKPY KLLS EKEKEIYRWP IKESLKTMLA WGWRIERTRE GDSMALYNRT RRISQTSQVS VDAAHG YSP RAIDMSNVTL SRDLHAMAEM MAENYHNIWA KKKKMELESK GGGNHPLLVP YDTLTAK EK AKDREKAQDI LKFLQINGYA VSRGFKDLEL DTPSIEKRFA YSFLQQLIRY VDEAHQYI L EFDGGSRGKG EHFPYEQEIK FFAKVVLPLI DQYFKNHRLY FLSAASRPLC SGGHASNKE KEMVTSLFCK LGVLVRHRIS LFGNDATSIV NCLHILGQTL DARTVMKTGL ESVKSALRAF LDNAAEDLE KTMENLKQGQ FTHTRNQPKG VTQIINYTTV ALLPMLSSLF EHIGQHQFGE D LILEDVQV SCYRILTSLY ALGTSKSIYV ERQRSALGEC LAAFAGAFPV AFLETHLDKH NI YSIYNTK SSRERAALSL PTNVEDVCPN IPSLEKLMEE IVELAESGIR YTQMPHVMEV ILP MLCSYM SRWWEHGPEN NPERAEMCCT ALNSEHMNTL LGNILKIIYN NLGIDEGAWM KRLA VFSQP IINKVKPQLL KTHFLPLMEK LKKKAATVVS EEDHLKAEAR GDMSEAELLI LDEFT TLAR DLYAFYPLLI RFVDYNRAKW LKEPNPEAEE LFRMVAEVFI YWSKSHNFKR EEQNFV VQN EINNMSFLIT DTKSKMSKAA VSDQERKKMK RKGDRYSMQT SLIVAALKRL LPIGLNI CA PGDQELIALA KNRFSLKDTE DEVRDIIRSN IHLQGKLEDP AIRWQMALYK DLPNRTDD T SDPEKTVERV LDIANVLFHL EQKSKRVGRR HYCLVEHPQR SKKAVWHKLL SKQRKRAVV ACFRMAPLYN LPRHRAVNLF LQGYEKSWIE TEEHYFEDKL IEDLAKPGAE PPEEDEGTKR VDPLHQLIL LFSRTALTEK CKLEEDFLYM AYADIMAKSC HDEEDDDGEE EVKSFEEKEM E KQKLLYQQ ARLHDRGAAE MVLQTISASK GETGPMVAAT LKLGIAILNG GNSTVQQKML DY LKEKKDV GFFQSLAGLM QSCSVLDLNA FERQNKAEGL GMVTEEGSGE KVLQDDEFTC DLF RFLQLL CEGHNSDFQN YLRTQTGNNT TVNIIISTVD YLLRVQESIS DFYWYYSGKD VIDE QGQRN FSKAIQVAKQ VFNTLTEYIQ GPCTGNQQSL AHSRLWDAVV GFLHVFAHMQ MKLSQ DSSQ IELLKELMDL QKDMVVMLLS MLEGNVVNGT IGKQMVDMLV ESSNNVEMIL KFFDMF LKL KDLTSSDTFK EYDPDGKGVI SKRDFHKAME SHKHYTQSET EFLLSCAETD ENETLDY EE FVKRFHEPAK DIGFNVAVLL TNLSEHMPND TRLQTFLELA ESVLNYFQPF LGRIEIMG S AKRIERVYFE ISESSRTQWE KPQVKESKRQ FIFDVVNEGG EKEKMELFVN FCEDTIFEM QLAAQISESD LNERSANKEE SEKERPEEQG PRMAFFSILT VRSALFALRY NILTLMRMLS LKSLKKQMK KVKKMTVKDM VTAFFSSYWS IFMTLLHFVA SVFRGFFRII CSLLLGGSLV E GAKKIKVA ELLANMPDPT QDEVRGDGEE GERKPLEAAL PSEDLTDLKE LTEESDLLSD IF GLDLKRE GGQYKLIPHN PNAGLSDLMS NPVPMPEVQE KFQEQKAKEE EKEEKEETKS EPE KAEGED GEKEEKAKED KGKQKLRQLH THRYGEPEVP ESAFWKKIIA YQQKLLNYFA RNFY NMRML ALFVAFAINF ILLFYKVSTS SVVEGKELPT RSSSENAKVT SLDSSSHRII AVHYV LEES SGYMEPTLRI LAILHTVISF FCIIGYYCLK VPLVIFKREK EVARKLEFDG LYITEQ PSE DDIKGQWDRL VINTQSFPNN YWDKFVKRKV MDKYGEFYGR DRISELLGMD KAALDFS DA REKKKPKKDS SLSAVLNSID VKYQMWKLGV VFTDNSFLYL AWYMTMSVLG HYNNFFFA A HLLDIAMGFK TLRTILSSVT HNGKQLVLTV GLLAVVVYLY TVVAFNFFRK FYNKSEDGD TPDMKCDDML TCYMFHMYVG VRAGGGIGDE IEDPAGDEYE IYRIIFDITF FFFVIVILLA IIQGLIIDA FGELRDQQEQ VKEDMETKCF ICGIGNDYFD TVPHGFETHT LQEHNLANYL F FLMYLINK DETEHTGQES YVWKMYQERC WEFFPAGDCF RKQYEDQLN

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: UltrAuFoil R0.6/1
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 34247
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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