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- EMDB-40432: Cryo-EM Structure of RyR1 + AMP (Local Refinement of TMD) -

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Basic information

Entry
Database: EMDB / ID: EMD-40432
TitleCryo-EM Structure of RyR1 + AMP (Local Refinement of TMD)
Map data
Sample
  • Complex: RyR1 in complex with FKBP12.6
    • Protein or peptide: Ryanodine receptor 1
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: ZINC ION
KeywordsCalcium ion channel / skeletal muscle / nucleotide / homotetramer / TRANSPORT PROTEIN
Function / homology
Function and homology information


ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / organelle membrane / cellular response to caffeine / outflow tract morphogenesis ...ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / skin development / organelle membrane / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / toxic substance binding / voltage-gated calcium channel activity / smooth endoplasmic reticulum / skeletal muscle fiber development / striated muscle contraction / release of sequestered calcium ion into cytosol / muscle contraction / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / calcium ion transmembrane transport / calcium channel activity / sarcolemma / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / identical protein binding / membrane
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 / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 1
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsCholak S / Saville JW / Zhu X / Berezuk AM / Tuttle KS / Haji-Ghassemi O / Van Petegem F / Subramaniam S
Funding support Canada, 2 items
OrganizationGrant numberCountry
Canada Excellence Research Chair Award Canada
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Structure / Year: 2023
Title: Allosteric modulation of ryanodine receptor RyR1 by nucleotide derivatives.
Authors: Spencer Cholak / James W Saville / Xing Zhu / Alison M Berezuk / Katharine S Tuttle / Omid Haji-Ghassemi / Francisco J Alvarado / Filip Van Petegem / Sriram Subramaniam /
Abstract: The coordinated release of Ca from the sarcoplasmic reticulum (SR) is critical for excitation-contraction coupling. This release is facilitated by ryanodine receptors (RyRs) that are embedded in the ...The coordinated release of Ca from the sarcoplasmic reticulum (SR) is critical for excitation-contraction coupling. This release is facilitated by ryanodine receptors (RyRs) that are embedded in the SR membrane. In skeletal muscle, activity of RyR1 is regulated by metabolites such as ATP, which upon binding increase channel open probability (P). To obtain structural insights into the mechanism of RyR1 priming by ATP, we determined several cryo-EM structures of RyR1 bound individually to ATP-γ-S, ADP, AMP, adenosine, adenine, and cAMP. We demonstrate that adenine and adenosine bind RyR1, but AMP is the smallest ATP derivative capable of inducing long-range (>170 Å) structural rearrangements associated with channel activation, establishing a structural basis for key binding site interactions that are the threshold for triggering quaternary structural changes. Our finding that cAMP also induces these structural changes and results in increased channel opening suggests its potential role as an endogenous modulator of RyR1 conductance.
History
DepositionApr 10, 2023-
Header (metadata) releaseMay 24, 2023-
Map releaseMay 24, 2023-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40432.png

Downloads & links

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Map

FileDownload / File: emd_40432.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.29 Å/pix.
x 400 pix.
= 515.2 Å		1.29 Å/pix.
x 400 pix.
= 515.2 Å		1.29 Å/pix.
x 400 pix.
= 515.2 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.288 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.192
Minimum - Maximum-1.8911746 - 3.0576043
Average (Standard dev.)-0.0013412113 (±0.058949437)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 515.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_40432_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Histogram (log scale)

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Half map: #2

Fileemd_40432_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : RyR1 in complex with FKBP12.6

EntireName: RyR1 in complex with FKBP12.6
Components
  • Complex: RyR1 in complex with FKBP12.6
    • Protein or peptide: Ryanodine receptor 1
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: RyR1 in complex with FKBP12.6

SupramoleculeName: RyR1 in complex with FKBP12.6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Ryanodine receptor 1

MacromoleculeName: Ryanodine receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 565.908625 KDa
SequenceString: MGDGGEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSRMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT MHPASKQRSE G EKVRVGDD ...String:
MGDGGEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSRMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT MHPASKQRSE G EKVRVGDD LILVSVSSER YLHLSTASGE LQVDASFMQT LWNMNPICSC CEEGYVTGGH VLRLFHGHMD ECLTISAADS DD QRRLVYY EGGAVCTHAR SLWRLEPLRI SWSGSHLRWG QPLRIRHVTT GRYLALTEDQ GLVVVDACKA HTKATSFCFR VSK EKLDTA PKRDVEGMGP PEIKYGESLC FVQHVASGLW LTYAAPDPKA LRLGVLKKKA ILHQEGHMDD ALFLTRCQQE ESQA ARMIH STAGLYNQFI KGLDSFSGKP RGSGPPAGPA LPIEAVILSL QDLIGYFEPP SEELQHEEKQ SKLRSLRNRQ SLFQE EGML SLVLNCIDRL NVYTTAAHFA EYAGEEAAES WKEIVNLLYE LLASLIRGNR ANCALFSTNL DWVVSKLDRL EASSGI LEV LYCVLIESPE VLNIIQENHI KSIISLLDKH GRNHKVLDVL CSLCVCNGVA VRSNQDLITE NLLPGRELLL QTNLINY VT SIRPNIFVGR AEGSTQYGKW YFEVMVDEVV PFLTAQATHL RVGWALTEGY SPYPGGGEGW GGNGVGDDLY SYGFDGLH L WTGHVARPVT SPGQHLLAPE DVVSCCLDLS VPSISFRING CPVQGVFEAF NLDGLFFPVV SFSAGVKVRF LLGGRHGEF KFLPPPGYAP CHEAVLPRER LRLEPIKEYR REGPRGPHLV GPSRCLSHTD FVPCPVDTVQ IVLPPHLERI REKLAENIHE LWALTRIEQ GWTYGPVRDD NKRLHPCLVN FHSLPEPERN YNLQMSGETL KTLLALGCHV GMADEKAEDN LKKTKLPKTY M MSNGYKPA PLDLSHVRLT PAQTTLVDRL AENGHNVWAR DRVAQGWSYS AVQDIPARRN PRLVPYRLLD EATKRSNRDS LC QAVRTLL GYGYNIEPPD QEPSQVENQS RWDRVRIFRA EKSYTVQSGR WYFEFEAVTT GEMRVGWARP ELRPDVELGA DEL AYVFNG HRGQRWHLGS EPFGRPWQSG DVVGCMIDLT ENTIIFTLNG EVLMSDSGSE TAFREIEIGD GFLPVCSLGP GQVG HLNLG QDVSSLRFFA ICGLQEGFEP FAINMQRPVT TWFSKSLPQF EPVPPEHPHY EVARMDGTVD TPPCLRLAHR TWGSQ NSLV EMLFLRLSLP VQFHQHFRCT AGATPLAPPG LQPPAEDEAR AAEPDPDYEN LRRSAGGWGE AEGGKEGTAK EGTPGG TPQ PGVEAQPVRA ENEKDATTEK NKKRGFLFKA KKAAMMTQPP ATPALPRLPH DVVPADNRDD PEIILNTTTY YYSVRVF AG QEPSCVWVGW VTPDYHQHDM NFDLSKVRAV TVTMGDEQGN VHSSLKCSNC YMVWGGDFVS PGQQGRISHT DLVIGCLV D LATGLMTFTA NGKESNTFFQ VEPNTKLFPA VFVLPTHQNV IQFELGKQKN IMPLSAAMFL SERKNPAPQC PPRLEVQML MPVSWSRMPN HFLQVETRRA GERLGWAVQC QDPLTMMALH IPEENRCMDI LELSERLDLQ RFHSHTLRLY RAVCALGNNR VAHALCSHV DQAQLLHALE DAHLPGPLRA GYYDLLISIH LESACRSRRS MLSEYIVPLT PETRAITLFP PGRKGGNARR H GLPGVGVT TSLRPPHHFS PPCFVAALPA AGVAEAPARL SPAIPLEALR DKALRMLGEA VRDGGQHARD PVGGSVEFQF VP VLKLVST LLVMGIFGDE DVKQILKMIE PEVFTEEEEE EEEEEEEEEE EEEDEEEKEE DEEEEEKEDA EKEEEEAPEG EKE DLEEGL LQMKLPESVK LQMCNLLEYF CDQELQHRVE SLAAFAERYV DKLQANQRSR YALLMRAFTM SAAETARRTR EFRS PPQEQ INMLLHFKDE ADEEDCPLPE DIRQDLQDFH QDLLAHCGIQ LEGEEEEPEE ETSLSSRLRS LLETVRLVKK KEEKP EEEL PAEEKKPQSL QELVSHMVVR WAQEDYVQSP ELVRAMFSLL HRQYDGLGEL LRALPRAYTI SPSSVEDTMS LLECLG QIR SLLIVQMGPQ EENLMIQSIG NIMNNKVFYQ HPNLMRALGM HETVMEVMVN VLGGGETKEI RFPKMVTSCC RFLCYFC RI SRQNQRSMFD HLSYLLENSG IGLGMQGSTP LDVAAASVID NNELALALQE QDLEKVVSYL AGCGLQSCPM LLAKGYPD I GWNPCGGERY LDFLRFAVFV NGESVEENAN VVVRLLIRKP ECFGPALRGE GGSGLLAAIE EAIRISEDPA RDGPGVRRD RRREHFGEEP PEENRVHLGH AIMSFYAALI DLLGRCAPEM HLIQAGKGEA LRIRAILRSL VPLDDLVGII SLPLQIPTLG KDGALVQPK MSASFVPDHK ASMVLFLDRV YGIENQDFLL HVLDVGFLPD MRAAASLDTA TFSTTEMALA LNRYLCLAVL P LITKCAPL FAGTEHRAIM VDSMLHTVYR LSRGRSLTKA QRDVIEDCLM ALCRYIRPSM LQHLLRRLVF DVPILNEFAK MP LKLLTNH YERCWKYYCL PTGWANFGVT SEEELHLTRK LFWGIFDSLA HKKYDQELYR MAMPCLCAIA GALPPDYVDA SYS SKAEKK ATVDAEGNFD PRPVETLNVI IPEKLDSFIN KFAEYTHEKW AFDKIQNNWS YGENVDEELK THPMLRPYKT FSEK DKEIY RWPIKESLKA MIAWEWTIEK AREGEEERTE KKKTRKISQT AQTYDPREGY NPQPPDLSGV TLSRELQAMA EQLAE NYHN TWGRKKKQEL EAKGGGTHPL LVPYDTLTAK EKARDREKAQ ELLKFLQMNG YAVTRGLKDM ELDTSSIEKR FAFGFL QQL LRWMDISQEF IAHLEAVVSS GRVEKSPHEQ EIKFFAKILL PLINQYFTNH CLYFLSTPAK VLGSGGHASN KEKEMIT SL FCKLAALVRH RVSLFGTDAP AVVNCLHILA RSLDARTVMK SGPEIVKAGL RSFFESASED IEKMVENLRL GKVSQART Q VKGVGQNLTY TTVALLPVLT TLFQHIAQHQ FGDDVILDDV QVSCYRTLCS IYSLGTTKNT YVEKLRPALG ECLARLAAA MPVAFLEPQL NEYNACSVYT TKSPRERAIL GLPNSVEEMC PDIPVLDRLM ADIGGLAESG ARYTEMPHVI EITLPMLCSY LPRWWERGP EAPPPALPAG APPPCTAVTS DHLNSLLGNI LRIIVNNLGI DEATWMKRLA VFAQPIVSRA RPELLHSHFI P TIGRLRKR AGKVVAEEEQ LRLEAKAEAE EGELLVRDEF SVLCRDLYAL YPLLIRYVDN NRAHWLTEPN ANAEELFRMV GE IFIYWSK SHNFKREEQN FVVQNEINNM SFLTADSKSK MAKAGDAQSG GSDQERTKKK RRGDRYSVQT SLIVATLKKM LPI GLNMCA PTDQDLIMLA KTRYALKDTD EEVREFLQNN LHLQGKVEGS PSLRWQMALY RGLPGREEDA DDPEKIVRRV QEVS AVLYH LEQTEHPYKS KKAVWHKLLS KQRRRAVVAC FRMTPLYNLP THRACNMFLE SYKAAWILTE DHSFEDRMID DLSKA GEQE EEEEEVEEKK PDPLHQLVLH FSRTALTEKS KLDEDYLYMA YADIMAKSCH LEEGGENGEA EEEEVEVSFE EKEMEK QRL LYQQSRLHTR GAAEMVLQMI SACKGETGAM VSSTLKLGIS ILNGGNAEVQ QKMLDYLKDK KEVGFFQSIQ ALMQTCS VL DLNAFERQNK AEGLGMVNED GTVINRQNGE KVMADDEFTQ DLFRFLQLLC EGHNNDFQNY LRTQTGNTTT INIIICTV D YLLRLQESIS DFYWYYSGKD VIEEQGKRNF SKAMSVAKQV FNSLTEYIQG PCTGNQQSLA HSRLWDAVVG FLHVFAHMM MKLAQDSSQI ELLKELLDLQ KDMVVMLLSL LEGNVVNGMI ARQMVDMLVE SSSNVEMILK FFDMFLKLKD IVGSEAFQDY VTDPRGLIS KKDFQKAMDS QKQFTGPEIQ FLLSCSEADE NEMINFEEFA NRFQEPARDI GFNVAVLLTN LSEHVPHDPR L RNFLELAE SILEYFRPYL GRIEIMGASR RIERIYFEIS ETNRAQWEMP QVKESKRQFI FDVVNEGGEA EKMELFVSFC ED TIFEMQI AAQISEPEGE PEADEDEGMG EAAAEGAEEG AAGAEGAAGT VAAGATARLA AAAARALRGL SYRSLRRRVR RLR RLTARE AATALAALLW AVVARAGAAG AGAAAGALRL LWGSLFGGGL VEGAKKVTVT ELLAGMPDPT SDEVHGEQPA GPGG DADGA GEGEGEGDAA EGDGDEEVAG HEAGPGGAEG VVAVADGGPF RPEGAGGLGD MGDTTPAEPP TPEGSPILKR KLGVD GEEE ELVPEPEPEP EPEPEKADEE NGEKEEVPEA PPEPPKKAPP SPPAKKEEAG GAGMEFWGEL EVQRVKFLNY LSRNFY TLR FLALFLAFAI NFILLFYKVS DSPPGEDDME GSAAGDLAGA GSGGGSGWGS GAGEEAEGDE DENMVYYFLE ESTGYME PA LWCLSLLHTL VAFLCIIGYN CLKVPLVIFK REKELARKLE FDGLYITEQP GDDDVKGQWD RLVLNTPSFP SNYWDKFV K RKVLDKHGDI FGRERIAELL GMDLASLEIT AHNERKPDPP PGLLTWLMSI DVKYQIWKFG VIFTDNSFLY LGWYMVMSL LGHYNNFFFA AHLLDIAMGV KTLRTILSSV THNGKQLVMT VGLLAVVVYL YTVVAFNFFR KFYNKSEDED EPDMKCDDMM TCYLFHMYV GVRAGGGIGD EIEDPAGDEY ELYRVVFDIT FFFFVIVILL AIIQGLIIDA FGELRDQQEQ VKEDMETKCF I CGIGSDYF DTTPHGFETH TLEEHNLANY MFFLMYLINK DETEHTGQES YVWKMYQERC WDFFPAGDCF RKQYEDQLS

UniProtKB: Ryanodine receptor 1

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Macromolecule #2: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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Macromolecule #3: ZINC ION

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

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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: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 96000
Sample stageSpecimen 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 modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 133836
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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