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- EMDB-22616: Cryo-EM structure of rabbit RyR1 in the presence of AMP-PCP in na... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-22616 | |||||||||||||||||||||
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Title | Cryo-EM structure of rabbit RyR1 in the presence of AMP-PCP in nanodisc | |||||||||||||||||||||
![]() | Masked full map | |||||||||||||||||||||
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![]() | Ryanodine Receptor / RyR1 / Intracellular Calcium channel / Excitation-Contraction coupling / TRANSPORT PROTEIN / ATP | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | |||||||||||||||||||||
![]() | Nayak AR / Samso M | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Ca inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM. Authors: Ashok R Nayak / Montserrat Samsó / ![]() Abstract: Activation of the intracellular Ca channel ryanodine receptor (RyR) triggers a cytosolic Ca surge, while elevated cytosolic Ca inhibits the channel in a negative feedback mechanism. Cryogenic ...Activation of the intracellular Ca channel ryanodine receptor (RyR) triggers a cytosolic Ca surge, while elevated cytosolic Ca inhibits the channel in a negative feedback mechanism. Cryogenic electron microscopy of rabbit RyR1 embedded in nanodiscs under partially inactivating Ca conditions revealed an open and a closed-inactivated conformation. Ca binding to the high-affinity site engages the central and C-terminal domains into a block, which pries the S6 four-helix bundle open. Further rotation of this block pushes S6 toward the central axis, closing (inactivating) the channel. Main characteristics of the Ca-inactivated conformation are downward conformation of the cytoplasmic assembly and tightly knit subunit interface contributed by a fully occupied Ca activation site, two inter-subunit resolved lipids, and two salt bridges between the EF hand domain and the S2-S3 loop validated by disease-causing mutations. The structural insight illustrates the prior Ca activation prerequisite for Ca inactivation and provides for a seamless transition from inactivated to closed conformations. | |||||||||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 31.3 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 34.5 KB 34.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.8 KB | Display | ![]() |
Images | ![]() | 137.5 KB | ||
Masks | ![]() | 307.5 MB | ![]() | |
Filedesc metadata | ![]() | 9.2 KB | ||
Others | ![]() ![]() ![]() ![]() | 240.2 MB 239.6 MB 28 MB 28 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7k0tMC ![]() 7tdgC ![]() 7tdhC ![]() 7tdiC ![]() 7tdjC ![]() 7tdkC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Masked full map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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-Additional map: Unfiltered and unmasked half map1 up to Nyquist frequency
File | emd_22616_additional_1.map | ||||||||||||
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Annotation | Unfiltered and unmasked half map1 up to Nyquist frequency | ||||||||||||
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-Additional map: Unfiltered and unmasked half map2 up to Nyquist frequency
File | emd_22616_additional_2.map | ||||||||||||
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Annotation | Unfiltered and unmasked half map2 up to Nyquist frequency | ||||||||||||
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-Half map: Masked half map1
File | emd_22616_half_map_1.map | ||||||||||||
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Annotation | Masked half map1 | ||||||||||||
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-Half map: Masked half map2
File | emd_22616_half_map_2.map | ||||||||||||
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Annotation | Masked half map2 | ||||||||||||
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Sample components
-Entire : Rabbit RyR1 with AMP-PCP
Entire | Name: Rabbit RyR1 with AMP-PCP |
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Components |
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-Supramolecule #1: Rabbit RyR1 with AMP-PCP
Supramolecule | Name: Rabbit RyR1 with AMP-PCP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: Purified RyR1 was reconstituted with membrane scaffold protein MSP1E3D1, and POPC. |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 2.26 MDa |
-Macromolecule #1: RyR1
Macromolecule | Name: RyR1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 533.66325 KDa |
Sequence | String: 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 (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) EL GKQKNIMPLS AAMFLSERKN PAPQCPPRLE VQMLMPVSWS RMPNHFLQVE TRRAGERLGW AVQCQDPLTM MALHIPEE N RCMDILELSE RLDLQRFHSH TLRLYRAVCA LGNNRVAHAL CSHVDQAQLL HALEDAHLPG PLRAGYYDLL ISIHLESAC RSRRSMLSEY IVPLTPETRA ITLFPPGRKG GNARRHGLPG VGVTTSLRPP HHFSPPCFVA ALPAAGVAEA PARLSPAIPL EALRDKALR MLGEAVRDGG QHARDPVGGS VEFQFVPVLK LVSTLLVMGI FGDEDVKQIL KMIEPEVFTE EEEEEEEEEE E EEEEEEDE EEKEEDEEEE EKEDAEKEEE EAPEGEKEDL EEGLLQMKLP ESVKLQMCNL LEYFCDQELQ HRVESLAAFA ER YVDKLQA NQRSRYALLM RAFTMSAAET ARRTREFRSP PQEQINMLLH FKDEADEEDC PLPEDIRQDL QDFHQDLLAH CGI QLEGEE EEPEEETSLS SRLRSLLETV RLVKKKEEKP EEELPAEEKK PQSLQELVSH MVVRWAQEDY VQSPELVRAM FSLL HRQYD GLGELLRALP RAYTISPSSV EDTMSLLECL GQIRSLLIVQ MGPQEENLMI QSIGNIMNNK VFYQHPNLMR ALGMH ETVM EVMVNVLGGG ETKEIRFPKM VTSCCRFLCY FCRISRQNQR SMFDHLSYLL ENSGIGLGMQ GSTPLDVAAA SVIDNN ELA LALQEQDLEK VVSYLAGCGL QSCPMLLAKG YPDIGWNPCG GERYLDFLRF AVFVNGESVE ENANVVVRLL IRKPECF GP ALRGEGGSGL LAAIEEAIRI SEDPARDGPG VRRDRRREHF GEEPPEENRV HLGHAIMSFY AALIDLLGRC APEMHLIQ A GKGEALRIRA ILRSLVPLDD LVGIISLPLQ IPTLGKDGAL V(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)CAIAGALP PDYVDASYSS KAEKKATVDA EGNFDPRPVE TLNVIIPEKL DSFINKFAEY THEKWAFDKI QN NWSYGEN VDEELKTHPM LRPYKTFSEK DKEIYRWPIK ESLKAMIAWE WTIEKAREGE EERTEKKKTR KISQTAQTYD PRE GYNPQP PDLSGVTLSR ELQAMAEQLA ENYHNTWGRK KKQELEAKGG GTHPLLVPYD TLTAKEKARD REKAQELLKF LQMN GYAVT RGL(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) 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(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)KSK KAVWHKLLSK QRRRAVVACF RMTPLYNLPT HRACNMFLES YKAAWILTED HSFEDRMIDD LSKAGEQ EE EEEEVEEKKP DPLHQLVLHF SRTALTEKSK LDEDYLYMAY ADIMAKSCHL EEGGENGEAE EEEVEVSFEE KEMEKQRL L YQQSRLHTRG AAEMVLQMIS ACKGETGAMV SSTLKLGISI LNGGNAEVQQ KMLDYLKDKK EVGFFQSIQA LMQTCSVLD LNAFERQNKA EGLGMVNEDG TVINRQNGEK VMADDEFTQD LFRFLQLLCE GHNNDFQNYL RTQTGNTTTI NIIICTVDYL LRLQESISD FYWYYSGKDV IEEQGKRNFS KAMSVAKQVF NSLTEYIQGP CTGNQQSLAH SRLWDAVVGF LHVFAHMMMK L AQDSSQIE LLKELLDLQK DMVVMLLSLL EGNVVNGMIA RQMVDMLVES SSNVEMILKF FDMFLKLKDI VGSEAFQDYV TD PRGLISK KDFQKAMDSQ KQFTGPEIQF LLSCSEADEN EMINFEEFAN RFQEPARDIG FNVAVLLTNL SEHVPHDPRL RNF LELAES ILEYFRPYLG RIEIMGASRR IERIYFEISE TNRAQWEMPQ VKESKRQFIF DVVNEGGEAE KMELFVSFCE DTIF EMQIA AQISEPEGEP EADEDEGMGE AAAEGAEEGA AGAEGAAGTV AAGATARLAA AAARALRGLS YRSLRRRVRR LRRLT AREA ATALAALLWA VVARAGAAGA GAAAGALRLL WGSLFGGGLV EGAKKVTVTE LLAGMPDPTS DEVHGEQPAG PGGDAD GAG EGEGEGDAAE GDGDEEVAGH EAGPGGAEGV VAVADGGPFR PEGAGGLGDM GDTTPAEPPT PEGSPILKRK LGVDGEE EE LVPEPEPEPE PEPEKADEEN GEKEEVPEAP PEPPKKAPPS PPAKKEEAGG AGMEFWGELE VQRVKFLNYL SRNFYTLR F LALFLAFAIN FILLFYKVSD SPPGEDDMEG SAAGDLAGAG SGGGSGWGSG AGEEAEGDED ENMVYYFLEE STGYMEPAL WCLSLLHTLV AFLCIIGYNC LKVPLVIFKR EKELARKLEF DGLYITEQPG DDDVKGQWDR LVLNTPSFPS NYWDKFVKRK VLDKHGDIF GRERIAELLG MDLASLEITA HNERKPDPPP GLLTWLMSID VKYQIWKFGV IFTDNSFLYL GWYMVMSLLG H YNNFFFAA HLLDIAMGVK TLRTILSSVT HNGKQLVMTV GLLAVVVYLY TVVAFNFFRK FYNKSEDEDE PDMKCDDMMT CY LFHMYVG VRAGGGIGDE IEDPAGDEYE LYRVVFDITF FFFVIVILLA IIQGLIIDAF GELRDQQEQV KEDMETKCFI CGI GSDYFD TTPHGFETHT LEEHNLANYM FFLMYLINKD ETEHTGQESY VWKMYQERCW DFFPAGDCFR KQYEDQLS |
-Macromolecule #2: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
Macromolecule | Name: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 4 / Formula: ACP |
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Molecular weight | Theoretical: 505.208 Da |
Chemical component information | ![]() ChemComp-ACP: |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 4.35 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Sample was blotted for 1 second on both sides with Whatman hardened ashless filter paper with blot force 2.. | |||||||||||||||||||||
Details | Purified RyR1 was reconstituted with membrane scaffold protein, MSP1E3D1, and POPC in 1:2:50 molar ratio. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 1959 / Average electron dose: 70.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-7k0t: |