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- EMDB-9825: Structure of RyR2 (F/A/Ca2+ dataset) -

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Basic information

Entry
Database: EMDB / ID: EMD-9825
TitleStructure of RyR2 (F/A/Ca2+ dataset)
Map data
Sample
  • Complex: RyR2 in complex with FKBP12.6Ryanodine receptor 2
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: RyR2Ryanodine receptor 2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
Keywordscryo-EM / MEMBRANE PROTEIN
Function / homology
Function and homology information


positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / cell communication by electrical coupling involved in cardiac conduction / response to redox state / protein maturation by protein folding / 'de novo' protein folding ...positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / cell communication by electrical coupling involved in cardiac conduction / response to redox state / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / negative regulation of phosphoprotein phosphatase activity / FK506 binding / positive regulation of axon regeneration / : / smooth muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / response to vitamin E / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / protein peptidyl-prolyl isomerization / T cell proliferation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / regulation of cytosolic calcium ion concentration / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to hydrogen peroxide / Stimuli-sensing channels / Z disc / positive regulation of cytosolic calcium ion concentration / protein refolding / transmembrane transporter binding / signaling receptor binding / membrane / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesSus scrofa (pig) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsChi XM / Gong DS
CitationJournal: Proc Natl Acad Sci U S A / Year: 2019
Title: Molecular basis for allosteric regulation of the type 2 ryanodine receptor channel gating by key modulators.
Authors: Ximin Chi / Deshun Gong / Kang Ren / Gewei Zhou / Gaoxingyu Huang / Jianlin Lei / Qiang Zhou / Nieng Yan /
Abstract: The type 2 ryanodine receptor (RyR2) is responsible for releasing Ca from the sarcoplasmic reticulum of cardiomyocytes, subsequently leading to muscle contraction. Here, we report 4 cryo-electron ...The type 2 ryanodine receptor (RyR2) is responsible for releasing Ca from the sarcoplasmic reticulum of cardiomyocytes, subsequently leading to muscle contraction. Here, we report 4 cryo-electron microscopy (cryo-EM) structures of porcine RyR2 bound to distinct modulators that, together with our published structures, provide mechanistic insight into RyR2 regulation. Ca alone induces a contraction of the central domain that facilitates the dilation of the S6 bundle but is insufficient to open the pore. The small-molecule agonist PCB95 helps Ca to overcome the barrier for opening. FKBP12.6 induces a relaxation of the central domain that decouples it from the S6 bundle, stabilizing RyR2 in a closed state even in the presence of Ca and PCB95. Although the channel is open when PCB95 is replaced by caffeine and adenosine 5'-triphosphate (ATP), neither of the modulators alone can sufficiently counter the antagonistic effect to open the channel. Our study marks an important step toward mechanistic understanding of the sophisticated regulation of this key channel whose aberrant activity engenders life-threatening cardiac disorders.
History
DepositionFeb 17, 2019-
Header (metadata) releaseDec 11, 2019-
Map releaseDec 11, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jh6
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9825.png

Downloads & links

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Map

FileDownload / File: emd_9825.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 400 pix.
= 522.616 Å		1.31 Å/pix.
x 400 pix.
= 522.616 Å		1.31 Å/pix.
x 400 pix.
= 522.616 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.031465713 - 0.07132422
Average (Standard dev.)0.0001274677 (±0.0036071609)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 522.616 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.306541.306541.30654
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z522.616522.616522.616
α/β/γ90.00090.00090.000
start NX/NY/NZ-51-35-11
NX/NY/NZ11110799
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0310.0710.000

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Supplemental data

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Sample components

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Entire : RyR2 in complex with FKBP12.6

EntireName: RyR2 in complex with FKBP12.6Ryanodine receptor 2
Components
  • Complex: RyR2 in complex with FKBP12.6Ryanodine receptor 2
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: RyR2Ryanodine receptor 2
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: RyR2 in complex with FKBP12.6

SupramoleculeName: RyR2 in complex with FKBP12.6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Peptidyl-prolyl cis-trans isomerase FKBP1B

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 1 / 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

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Macromolecule #2: RyR2

MacromoleculeName: RyR2 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 564.905625 KDa
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 VSLHVDAAFQ QTLWSVAPIS SGSEAAQGYL IGGDVLRLLH GH MDECLTV PSGEHGEEQR RTVHYEGGAV SVHARSLWRL ETLRVAWSGS HIRWGQPFRL RHVTTGKYLS LMEDKSLLLM DKE KADVKS TAFTFRSSKE KLDVGVRKEV DGMGTSEIKY GDSVCFIQHI GTGLWLTYQS VDVKSVRMGS IQRKAIMHHE GHMD DGLNL 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 VGISDEHAEE K VKKMKLPK NYQLTSGYKP APMDLSFIKL TPSQEAMVDK LAENAHNVWA RDRIRQGWTY GIQQDVKNRR NPRLVPYALL DD RTKKSNK DSLREAVRTL LGYGYNLEAP DQDHAARAEV CSGTGERFRI FRAEKTYAVK AGRWYFEFEA VTAGDMRVGW SRP GCQPDQ ELGSDERAFA FDGFKAQRWH QGNEHYGRSW QAGDVVGCMV DMTEHTMMFT LNGEILLDDS GSELAFKDFD VGDG FIPVC SLGVAQVGRM NFGKDVSTLK YFTICGLQEG YEPFAVNTNR DITMWLSKRL PQFLQVPSSH EHIEVTRIDG TIDSS PCLK VTQKSFGSQN SSTDIMFYRL SMPIECAEVF SKTSAGGIPG ASLFGPKNDL EDYDADSDFE VLMKTAHGHL VPDRVD KDK EATKPEFNNH KDYAQEKPSR LKQRFLLRRT KPDYSTSHSA RLTEDVLADD RDDYDYLMQT STYYYSVRIF PGQEPAN VW VGWITSDFHQ YDTAFDLDRV RTVTVTLGDE KGKVHESIKR SNCYMVCAGE SMSPGQGRNN NGLEIGCVVD AASGLLTF T ANGKDLSTYY QVEPSTKLFP AVFAQATSPN VFQFELGRIK NVMPLSAGLF KSEHKNPVPQ CPPRLHVQFL SHVLWSRMP NQFLKVDVSR ISERQGWLVQ CLEPLQFMSL HIPEENRSVD ILELTEQEEL LKFHYHTLRL YSAVCALGNH RVAHALCSHV DEPQLLYAI ENKYMPGLLR AGYYDLLIDI HLSSYATARL MMNNEFIVPM TEETKSITLF PDENKKHGLP GIGLSTSLRP R MQFSSPSF VSINNECYQY SPEFPLDILK AKTIQMLTEA VQEGSLHARD PVGGTTEFLF VPLIKLFYTL LIMGIFHNED LK HILQLIE PSVFKEAAGP EEESDTLEKE PCASEDSRLE GPAEEESKGG KRPKEGLLQM KLPEPVKLQM CLLLQYLCDC QVR HRIEAI VAFSDDFVAK LQDNQRFRYN EVMQALNMSA ALTARKTKEF RSPPQEQINM LLNFKDDKSE CPCPEEIRDQ LLDF HEDLM THCGIELDED GSLDGNSDLT IRGRLLSLVE KVTYLKKKQA EKLVESDSKK SSTLQQLISE TMVRWAQESV IEDPE LVRA MFVLLHRQYD GIGGLVRALP KTYTINGVSV EDTINLLASL GQIRSLLSVR MGKEEEKLMI RGLGDIMNNK VFYQHP NLM RALGMHETVM EVMVNVLGGG ESKEITFPKM VANCCRFLCY FCRISRQNQK AMFDHLSYLL ENSSVGLASP AMRGSTP LD VAAASVMDNN ELALALREPD LEKVVRYLAG CGLQSCQMLV SKGYPDIGWN PVEGERYLDF LRFAVFCNGE SVEENANV V VRLLIRRPEC FGPALRGEGG NGLLAAMEEA IKIAEDPSRD GPSPTSGSSK MPDTEGEEDD TIHMGNAIMT FYAALIDLL GRCAPEMHLI HAAKGEAIRI RSILRSLIPL GDLVGVISIA FQMPTIAKDG NVVEPDMSAG FCPDHKAAMV LFLDRVYGIE VQDFLLHLL EVGFLPDLRA AASLDTAALS ATDMALALNR YLCTAVLPLL TRCAPLFAGT EHHASLIDSL LHTVYRLSKG C SLTKAQRD SIEVCLLSIC GQLRPSMMQH LLRRLVFDVP LLNEHAKMPL KLLTNHYERC WKYYCLPGGW GNFGAASEEE LH LSRKLFW GIFDALSQKK YEQELFKLAL PCLSAVAGAL PPDYMESNYV SMMEKQSSMD SEGNFNPQPV DTSNITIPEK LEY FINKYA EHSHDKWSMD KLANGWIYGE IYSDSSKVQP LMKPYKLLSE KEKEIYRWPI KESLKTMLAW GWRIERTREG DSMA LYNRT RRISQTSQVS VDAAHGYSPR AIDMSNVTLS RDLHAMAEMM AENYHNIWAK KKKLELESKG GGNHPLLVPY DTLTA KEKA KDREKAQDIL KFLQINGYAV SRGFKDLELD TPSIEKRFAY SFLQQLIRYV DEAHQYILEF DGGSRSKGEH FPYEQE IKF FAKVVLPLID QYFKNHRLYF LSAASRPLCS GGHASNKEKE MVTSLFCKLG VLVRHRISLF GNDATSIVNC LHILGQT LD ARTVMKTGLE SVKSALRAFL DNAAEDLEKT MENLKQGQFT HTRNQPKGVT QIINYTTVAL LPMLSSLFEH IGQHQFGE D LILEDVQVSC YRILTSLYAL GTSKSIYVER QRSALGECLA AFAGAFPVAF LETHLDKHNI YSIYNTKSSR ERAALNLPT NVEDVCPNIP SLEKLMEEIV DLAESGIRYT QMPHVMEVVL PMLCSYMSRW WEHGPENNPG RAEMCCTALN SEHMNTLLGN ILKIIYNNL GIDEGAWMKR LAVFSQPIIN KVKPQLLKTH FLPLMEKLKK KAAMVVSEED HLKSEVRGDM SEAELLILDE F TTLARDLY AFYPLLIRFV DYNRAKWLKE PNPEAEDLFR MVAEVFIYWS KSHNFKREEQ NFVVQNEINN MSFLITDTKS KM SKAAVSD QERKKMKRKG DRYSMQTSLI VAALKRLLPI GLNICAPGDQ ELIALAKNRF SLKDTEDEVR DIIRSNIHLQ GKL EDPAIR WQMALYKDLP NRTEDTSDPE KTVERVLDIA NVLFHLEQKS TCMRRRYYSL VEHPQRSKKA VWHKLLSKQR KRAV VACFR MAPLYNLPRH RAVNLFLQGY EKSWIETEEH YFEDKLIEDL AKPGAVPPEE DEGTKRVDPL HQLILLFSRT ALTEK CKLE EDFLYMAYAD IMAKSCHDEE DDDGEEEVKS FEEKEMEKQK LLYQQARLHD RGAAEMVLQT ISASKGETGP MVAATL KLG IAILNGGNST VQQKMLEYLK EKKDVGFFQS LAGLMQSCSV LDLNAFERQN KAEGLGMVTE EGSGEKVLQD DEFTCDL FR FLQLLCEGHN SDFQNYLRTQ TGNNTTVNII ISTVDYLLRV QESISDFYWY YSGKDVIDEQ GQRNFSKAIQ VAKQVFNT L TEYIQGPCTG NQQSLAHSRL WDAVVGFLHV FAHMQMKLSQ DSSQIELLKE LMDLQKDMVV MLLSMLEGNV VNGTIGKQM VDMLVESSNN VEMILKFFDM FLKLKDLTSS DTFKEYDPDG KGVISKRDFH KAMESHKHYT QSETEFLLSC AETDENETLD YEEFVKRFH EPAKDIGFNV AVLLTNLSEH MPNDTRLQTF LELAESVLNY FQPFLGRIEI MGSAKRIERV YFEISESSRT Q WEKPQVKE SKRQFIFDVV NEGGEKEKME LFVNFCEDTI FEMQLAAQIS ESDLNERSAN KEESEKEKPE EQGPRMGFFS LV TVRSALL ALRYNVLTLM RMLSLKSLKK QMKKVKKMTV RDMVTAFFTS YWSVFMTLLH FAASVSRGFS RIIGGLLLGG SLV EGAKKI KVAELLANMP DPTQDEVRGD GDEGERKVLE GTLPSEDLTD LKELTEESDL LSDIFGLDLK REGGQYKLIP HNPN AGLSD LMSSPAPIPE VQEKFQEQKA KEEEKEEKEE NKSEPEKAEG EDGEKEEKAK EDKGKQKLRQ LHTHRYGEPE VPESA FWKK IIAYQQKLLN YFARNFYNMR MLALFVAFAI NFILLFYKVS TSSVVEGKEL PTRSSSENAN FGSLDSSSPR IIAVHY VLE ESSGYMEPTL RILAILHTVI SFFCIIGYYC LKVPLVIFKR EKEVARKLEF DGLYITEQPS EDDIKGQWDR LVINTQS FP NNYWDKFVKR KVMDKYGEFY GRDRISELLG MDKAALDFSD AREKKKPKKD SSLSAVLNSI DVKYQMWKLG VVFTDNSF L YLAWYMTMSV LGHYNNFFFA AHLLDIAMGF KTLRTILSSV THNGKQLVLT VGLLAVVVYL YTVVAFNFFR KFYNKSEDG DTPDMKCDDM LTCYMFHMYV GVRAGGGIGD EIEDPAGDEY EIYRIIFDIT FFFFVIVILL AIIQGLIIDA FGELRDQQEQ VKEDMETKC FICGIGNDYF DTVPHGFETH TLQEHNLANY LFFLMYLINK DETEHTGQES YVWKMYQERC WEFFPAGDCF R KQYEDQLN

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / 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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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 48.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 44288
FSC plot (resolution estimation)

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