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- EMDB-52090: transmembrane domain of ryanodine receptor1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-52090
Titletransmembrane domain of ryanodine receptor1
Map data
Sample
  • Complex: Transmembrane domain of ryanodine receptor1
    • Complex: Ryanodine receptor 1
      • Protein or peptide: ryanodine receptor
KeywordsIon channel / Ca2+ / tetramer / TRANSPORT PROTEIN
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi C / Efremov RG
Funding support Belgium, European Union, 3 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0H5916N Belgium
Research Foundation - Flanders (FWO)G054617N Belgium
European Research Council (ERC)726436European Union
CitationJournal: To Be Published
Title: Open-state RyR1 in 0.05% POPC micelles, in complex with a nanobody and FKBP
Authors: Li C / Efremov RG
History
DepositionNov 14, 2024-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52090.png

Downloads & links

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Map

FileDownload / File: emd_52090.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 336 pix.
= 488.544 Å		1.45 Å/pix.
x 336 pix.
= 488.544 Å		1.45 Å/pix.
x 336 pix.
= 488.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.454 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.62
Minimum - Maximum-2.2116752 - 3.862543
Average (Standard dev.)0.007582832 (±0.091007784)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 488.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52090_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52090_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_52090_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Transmembrane domain of ryanodine receptor1

EntireName: Transmembrane domain of ryanodine receptor1
Components
  • Complex: Transmembrane domain of ryanodine receptor1
    • Complex: Ryanodine receptor 1
      • Protein or peptide: ryanodine receptor

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Supramolecule #1: Transmembrane domain of ryanodine receptor1

SupramoleculeName: Transmembrane domain of ryanodine receptor1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Ryanodine receptor 1

SupramoleculeName: Ryanodine receptor 1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: all
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: ryanodine receptor

MacromoleculeName: ryanodine receptor / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
SequenceString: VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAGV ESSQGGGHR TLLYGHAILL RHAHSRMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT MHPASKQRSE GEKVRVGDDL I LVSVSSER ...String:
VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAGV ESSQGGGHR TLLYGHAILL RHAHSRMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT MHPASKQRSE GEKVRVGDDL I LVSVSSER YLHLSTASGE LQVDASFMQT LWNMNPICSC CEEGYVTGGH VLRLFHGHMD ECLTISAADS DDQRRLVYYE GG AVCTHAR SLWRLEPLRI SWSGSHLRWG QPLRIRHVTT GRYLALTEDQ GLVVVDACKA HTKATSFCFR VSKEKLDTAP KRD VEGMGP PEIKYGESLC FVQHVASGLW LTYAAPDPKA LRLGVLKKKA ILHQEGHMDD ALFLTRCQQE ESQAARMIHS TAGL YNQFI KGLDSFSGKP RGSGPPAGPA LPIEAVILSL QDLIGYFEPP SEELQHEEKQ SKLRSLRNRQ SLFQEEGMLS LVLNC IDRL NVYTTAAHFA EYAGEEAAES WKEIVNLLYE LLASLIRGNR ANCALFSTNL DWVVSKLDRL EASSGILEVL YCVLIE SPE VLNIIQENHI KSIISLLDKH GRNHKVLDVL CSLCVCNGVA VRSNQDLITE NLLPGRELLL QTNLINYVTS IRPNIFV GR AEGSTQYGKW YFEVMVDEVV PFLTAQATHL RVGWALTEGY SPYPGGGEGW GGNGVGDDLY SYGFDGLHLW TGHVARPV T SPGQHLLAPE DVVSCCLDLS VPSISFRING CPVQGVFEAF NLDGLFFPVV SFSAGVKVRF LLGGRHGEFK FLPPPGYAP CHEAVLPRER LRLEPIKEYR REGPRGPHLV GPSRCLSHTD FVPCPVDTVQ IVLPPHLERI REKLAENIHE LWALTRIEQG WTYGPVRDD NKRLHPCLVN FHSLPEPERN YNLQMSGETL KTLLALGCHV GMADEKAEDN LKKTKLPKTY MMSNGYKPAP L DLSHVRLT PAQTTLVDRL AENGHNVWAR DRVAQGWSYS AVQDIPARRN PRLVPYRLLD EATKRSNRDS LCQAVRTLLG YG YNIEPPD QEPSQVENQS RWDRVRIFRA EKSYTVQSGR WYFEFEAVTT GEMRVGWARP ELRPDVELGA DELAYVFNGH RGQ RWHLGS EPFGRPWQSG DVVGCMIDLT ENTIIFTLNG EVLMSDSGSE TAFREIEIGD GFLPVCSLGP GQVGHLNLGQ DVSS LRFFA ICGLQEGFEP FAINMQRPVT TWFSKSLPQF EPVPPEHPHY EVARMDGTVD TPPCLRLAHR TWGSQNSLVE MLFLR LSLP VQFHQHFRCT AGATPLAPPG LQPPAEDEAR AAEPDPDYEN LRRSAGGWGE AEGGKEGTAK EGTPGGTPQP GVEAQP VRA ENEKDATTEK NKKRGFLFKA KKAAMMTQPP ATPALPRLPH DVVPADNRDD PEIILNTTTY YYSVRVFAGQ EPSCVWV GW VTPDYHQHDM NFDLSKVRAV TVTMGDEQGN VHSSLKCSNC YMVWGGDFVS PGQQGRISHT DLVIGCLVDL ATGLMTFT A NGKESNTFFQ VEPNTKLFPA VFVLPTHQNV IQFELGKQKN IMPLSAAMFL SERKNPAPQC PPRLEVQMLM PVSWSRMPN HFLQVETRRA GERLGWAVQC QDPLTMMALH IPEENRCMDI LELSERLDLQ RFHSHTLRLY RAVCALGNNR VAHALCSHVD QAQLLHALE DAHLPGPLRA GYYDLLISIH LESACRSRRS MLSEYIVPLT PETRAITLFP PGRKGGNARR HGLPGVGVTT S LRPPHHFS PPCFVAALPA AGVAEAPARL SPAIPLEALR DKALRMLGEA VRDGGQHARD PVGGSVEFQF VPVLKLVSTL LV MGIFGDE DVKQILKMIE PEVFTEEEEE EEEEEEEEEE EEEDEEEKEE DEEEEEKEDA EKEEEEAPEG EKEDLEEGLL QMK LPESVK LQMCNLLEYF CDQELQHRVE SLAAFAERYV DKLQANQRSR YALLMRAFTM SAAETARRTR EFRSPPQEQI NMLL HFKDE ADEEDCPLPE DIRQDLQDFH QDLLAHCGIQ LEGEEEEPEE ETSLSSRLRS LLETVRLVKK KEEKPEEELP AEEKK PQSL QELVSHMVVR WAQEDYVQSP ELVRAMFSLL HRQYDGLGEL LRALPRAYTI SPSSVEDTMS LLECLGQIRS LLIVQM GPQ EENLMIQSIG NIMNNKVFYQ HPNLMRALGM HETVMEVMVN VLGGGETKEI RFPKMVTSCC RFLCYFCRIS RQNQRSM FD HLSYLLENSG IGLGMQGSTP LDVAAASVID NNELALALQE QDLEKVVSYL AGCGLQSCPM LLAKGYPDIG WNPCGGER Y LDFLRFAVFV NGESVEENAN VVVRLLIRKP ECFGPALRGE GGSGLLAAIE EAIRISEDPA RDGPGVRRDR RREHFGEEP PEENRVHLGH AIMSFYAALI DLLGRCAPEM HLIQAGKGEA LRIRAILRSL VPLDDLVGII SLPLQIPTLG KDGALVQPKM SASFVPDHK ASMVLFLDRV YGIENQDFLL HVLDVGFLPD MRAAASLDTA TFSTTEMALA LNRYLCLAVL PLITKCAPLF A GTEHRAIM VDSMLHTVYR LSRGRSLTKA QRDVIEDCLM ALCRYIRPSM LQHLLRRLVF DVPILNEFAK MPLKLLTNHY ER CWKYYCL PTGWANFGVT SEEELHLTRK LFWGIFDSLA HKKYDQELYR MAMPCLCAIA GALPPDYVDA SYSSKAEKKA TVD AEGNFD PRPVETLNVI IPEKLDSFIN KFAEYTHEKW AFDKIQNNWS YGENVDEELK THPMLRPYKT FSEKDKEIYR WPIK ESLKA MIAWEWTIEK AREGEEERTE KKKTRKISQT AQTYDPREGY NPQPPDLSGV TLSRELQAMA EQLAENYHNT WGRKK KQEL EAKGGGTHPL LVPYDTLTAK EKARDREKAQ ELLKFLQMNG YAVTRGLKDM ELDTSSIEKR FAFGFLQQLL RWMDIS QEF IAHLEAVVSS GRVEKSPHEQ EIKFFAKILL PLINQYFTNH CLYFLSTPAK VLGSGGHASN KEKEMITSLF CKLAALV RH RVSLFGTDAP AVVNCLHILA RSLDARTVMK SGPEIVKAGL RSFFESASED IEKMVENLRL GKVSQARTQV KGVGQNLT Y TTVALLPVLT TLFQHIAQHQ FGDDVILDDV QVSCYRTLCS IYSLGTTKNT YVEKLRPALG ECLARLAAAM PVAFLEPQL NEYNACSVYT TKSPRERAIL GLPNSVEEMC PDIPVLDRLM ADIGGLAESG ARYTEMPHVI EITLPMLCSY LPRWWERGPE APPPALPAG APPPCTAVTS DHLNSLLGNI LRIIVNNLGI DEATWMKRLA VFAQPIVSRA RPELLHSHFI PTIGRLRKRA G KVVAEEEQ LRLEAKAEAE EGELLVRDEF SVLCRDLYAL YPLLIRYVDN NRAHWLTEPN ANAEELFRMV GEIFIYWSKS HN FKREEQN FVVQNEINNM SFLTADSKSK MAKAGDAQSG GSDQERTKKK RRGDRYSVQT SLIVATLKKM LPIGLNMCAP TDQ DLIMLA KTRYALKDTD EEVREFLQNN LHLQGKVEGS PSLRWQMALY RGLPGREEDA DDPEKIVRRV QEVSAVLYHL EQTE HPYKS KKAVWHKLLS KQRRRAVVAC FRMTPLYNLP THRACNMFLE SYKAAWILTE DHSFEDRMID DLSKAGEQEE EEEEV EEKK PDPLHQLVLH FSRTALTEKS KLDEDYLYMA YADIMAKSCH LEEGGENGEA EEEEVEVSFE EKEMEKQRLL YQQSRL HTR GAAEMVLQMI SACKGETGAM VSSTLKLGIS ILNGGNAEVQ QKMLDYLKDK KEVGFFQSIQ ALMQTCSVLD LNAFERQ NK AEGLGMVNED GTVINRQNGE KVMADDEFTQ DLFRFLQLLC EGHNNDFQNY LRTQTGNTTT INIIICTVDY LLRLQESI S DFYWYYSGKD VIEEQGKRNF SKAMSVAKQV FNSLTEYIQG PCTGNQQSLA HSRLWDAVVG FLHVFAHMMM KLAQDSSQI ELLKELLDLQ KDMVVMLLSL LEGNVVNGMI ARQMVDMLVE SSSNVEMILK FFDMFLKLKD IVGSEAFQDY VTDPRGLISK KDFQKAMDS QKQFTGPEIQ FLLSCSEADE NEMINFEEFA NRFQEPARDI GFNVAVLLTN LSEHVPHDPR LRNFLELAES I LEYFRPYL GRIEIMGASR RIERIYFEIS ETNRAQWEMP QVKESKRQFI FDVVNEGGEA EKMELFVSFC EDTIFEMQIA AQ ISEPEGE PEADEDEGMG EAAAEGAEEG AAGAEGAAGT VAAGATARLA AAAARALRGL SYRSLRRRVR RLRRLTAREA ATA LAALLW AVVARAGAAG AGAAAGALRL LWGSLFGGGL VEGAKKVTVT ELLAGMPDPT SDEVHGEQPA GPGGDADGAG EGEG EGDAA EGDGDEEVAG HEAGPGGAEG VVAVADGGPF RPEGAGGLGD MGDTTPAEPP TPEGSPILKR KLGVDGEEEE LVPEP EPEP EPEPEKADEE NGEKEEVPEA PPEPPKKAPP SPPAKKEEAG GAGMEFWGEL EVQRVKFLNY LSRNFYTLRF LALFLA FAI NFILLFYKVS DSPPGEDDME GSAAGDLAGA GSGGGSGWGS GAGEEAEGDE DENMVYYFLE ESTGYMEPAL WCLSLLH TL VAFLCIIGYN CLKVPLVIFK REKELARKLE FDGLYITEQP GDDDVKGQWD RLVLNTPSFP SNYWDKFVKR KVLDKHGD I FGRERIAELL GMDLASLEIT AHNERKPDPP PGLLTWLMSI DVKYQIWKFG VIFTDNSFLY LGWYMVMSLL GHYNNFFFA AHLLDIAMGV KTLRTILSSV THNGKQLVMT VGLLAVVVYL YTVVAFNFFR KFYNKSEDED EPDMKCDDMM TCYLFHMYVG VRAGGGIGD EIEDPAGDEY ELYRVVFDIT FFFFVIVILL AIIQGLIIDA FGELRDQQEQ VKEDMETKCF ICGIGSDYFD T TPHGFETH TLEEHNLANY MFFLMYLINK DETEHTGQES YVWKMYQERC WDFFPAGDCF RKQYEDQLS

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER

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Image processing

DetailsThe movies were selected after MotionCor correction and CTF refinement with the parameters: total drift less than 30 angstrom and resolution better than 5 angstrom
Particle selectionDetails: Particles were picked by template picking in Cryosparc
CTF correctionSoftware - Name: RELION (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8rrw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.31) / Number images used: 80709
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 8 / Software - Name: RELION (ver. 4.1)

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