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- EMDB-9529: Cryo-EM structure of RyR2 in open state -

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Basic information

Entry
Database: EMDB / ID: EMD-9529
TitleCryo-EM structure of RyR2 in open state
Map dataopen state
Sample
  • Complex: RyR2
    • Protein or peptide: RyR2
  • Ligand: ZINC ION
KeywordsMembrane protein / Channel / TRANSPORT PROTEIN
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsPeng W / Wu JP
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2015CB9101012014, 2016YFA0500402, ZX09507003006 China
National Natural Science Foundation of Chinaproject 31321062, 31021002, 31611130036 China
CitationJournal: Science / Year: 2016
Title: Structural basis for the gating mechanism of the type 2 ryanodine receptor RyR2.
Authors: Wei Peng / Huaizong Shen / Jianping Wu / Wenting Guo / Xiaojing Pan / Ruiwu Wang / S R Wayne Chen / Nieng Yan /
Abstract: RyR2 is a high-conductance intracellular calcium (Ca) channel that controls the release of Ca from the sarco(endo)plasmic reticulum of a variety of cells. Here, we report the structures of RyR2 from ...RyR2 is a high-conductance intracellular calcium (Ca) channel that controls the release of Ca from the sarco(endo)plasmic reticulum of a variety of cells. Here, we report the structures of RyR2 from porcine heart in both the open and closed states at near-atomic resolutions determined using single-particle electron cryomicroscopy. Structural comparison reveals a breathing motion of the overall cytoplasmic region resulted from the interdomain movements of amino-terminal domains (NTDs), Helical domains, and Handle domains, whereas almost no intradomain shifts are observed in these armadillo repeats-containing domains. Outward rotations of the Central domains, which integrate the conformational changes of the cytoplasmic region, lead to the dilation of the cytoplasmic gate through coupled motions. Our structural and mutational characterizations provide important insights into the gating and disease mechanism of RyRs.
History
Header (metadata) releaseAug 17, 2016-
DepositionSep 8, 2016-
Map releaseOct 5, 2016-
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: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5goa
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9529.png

Downloads & links

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Map

FileDownload / File: emd_9529.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationopen state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 520 pix.
= 546. Å		1.05 Å/pix.
x 520 pix.
= 546. Å		1.05 Å/pix.
x 520 pix.
= 546. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.06714316 - 0.15507317
Average (Standard dev.)0.00033874772 (±0.005509373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 546.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z520520520
origin x/y/z0.0000.0000.000
length x/y/z546.000546.000546.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS520520520
D min/max/mean-0.0670.1550.000

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Supplemental data

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Mask #1

Fileemd_9529_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_9529_additional.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 : RyR2

EntireName: RyR2
Components
  • Complex: RyR2
    • Protein or peptide: RyR2
  • Ligand: ZINC ION

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Supramolecule #1: RyR2

SupramoleculeName: RyR2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Sus scrofa (pig)
Molecular weightTheoretical: 2.2 MDa

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Macromolecule #1: RyR2

MacromoleculeName: RyR2 / type: protein_or_peptide / ID: 1 / 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 #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / 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

Concentration0.1 mg/mL
BufferpH: 7.5
Details: 25 mM Tris, pH 7.5, 300 mM NaCl, 0.1 % Digitonin, 2 mM DTT, 5 mM EDTA, 20 uM CaCl2, 20 uM PCB 95 and protease inhibitors.
GridModel: Zhongjingkeyi Technology / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: Grids were immediately blotted for 1.5 s and flash-frozen in liquid ethane.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 44.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

2807

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 133196
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING
Final 3D classificationSoftware - Name: RELION (ver. 1.4)

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Atomic model buiding 1

RefinementSpace: RECIPROCAL
Output model

PDB-5goa:
Cryo-EM structure of RyR2 in open state

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