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- EMDB-22616: Cryo-EM structure of rabbit RyR1 in the presence of AMP-PCP in na... -

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Basic information

Entry
Database: EMDB / ID: EMD-22616
TitleCryo-EM structure of rabbit RyR1 in the presence of AMP-PCP in nanodisc
Map dataMasked full map
Sample
  • Complex: Rabbit RyR1 with AMP-PCP
    • Protein or peptide: RyR1Ryanodine receptor 1
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
  • Ligand: ZINC ION
Biological speciesOryctolagus cuniculus (rabbit) / rabbit (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsNayak AR / Samso M
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01 AR068431 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01 HL133182 United States
Other privateMDA 352845 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)HSSN261200800001E United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116789 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24 GM116790 United States
CitationJournal: Elife / Year: 2022
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
DepositionSep 5, 2020-
Header (metadata) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateMar 16, 2022-
Current statusMar 16, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7k0t
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22616.png

Downloads & links

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Map

FileDownload / File: emd_22616.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMasked full map
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.025
Minimum - Maximum-0.059354156 - 0.12836614
Average (Standard dev.)0.001059942 (±0.0056486824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 462.24002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z462.240462.240462.240
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-0.0590.1280.001

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Supplemental data

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Mask #1

Fileemd_22616_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Unfiltered and unmasked half map1 up to Nyquist frequency

Fileemd_22616_additional_1.map
AnnotationUnfiltered and unmasked half map1 up to Nyquist frequency
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Additional map: Unfiltered and unmasked half map2 up to Nyquist frequency

Fileemd_22616_additional_2.map
AnnotationUnfiltered and unmasked half map2 up to Nyquist frequency
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AxesZYX

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Half map: Masked half map1

Fileemd_22616_half_map_1.map
AnnotationMasked half map1
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Half map: Masked half map2

Fileemd_22616_half_map_2.map
AnnotationMasked half map2
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AxesZYX

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Sample components

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Entire : Rabbit RyR1 with AMP-PCP

EntireName: Rabbit RyR1 with AMP-PCP
Components
  • Complex: Rabbit RyR1 with AMP-PCP
    • Protein or peptide: RyR1Ryanodine receptor 1
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
  • Ligand: ZINC ION

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Supramolecule #1: Rabbit RyR1 with AMP-PCP

SupramoleculeName: Rabbit RyR1 with AMP-PCP / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: Purified RyR1 was reconstituted with membrane scaffold protein MSP1E3D1, and POPC.
Source (natural)Organism: Oryctolagus cuniculus (rabbit) / Strain: New Zealand White / Organ: Skeletal Muscle / Organelle: Sarcoplasmic Reticulum / Location in cell: Sarcoplasmic Reticulum membrane
Molecular weightExperimental: 2.26 MDa

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Macromolecule #1: RyR1

MacromoleculeName: RyR1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit) / Strain: New Zealand White / Organ: Skeletal Muscle
Molecular weightTheoretical: 533.66325 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 (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(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) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(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)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(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

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Macromolecule #2: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER

MacromoleculeName: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 4 / Formula: ACP
Molecular weightTheoretical: 505.208 Da
Chemical component information

ChemComp-ACP:
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / AMP-PCP, energy-carrying molecule analogue*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

Concentration4.35 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMMOPS (pH7.4)
635.0 mMPotassium ChlorideKCl
2.0 mMDithiothreitol
5.0 mMAMP-PCP
1.0 mMEGTA
1.0 mMEDTAEthylenediaminetetraacetic acid
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen 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..
DetailsPurified RyR1 was reconstituted with membrane scaffold protein, MSP1E3D1, and POPC in 1:2:50 molar ratio.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 52856
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: EMDB MAP
EMDB ID:

8391

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 21551
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7k0t:
Cryo-EM structure of rabbit RyR1 in the presence of AMP-PCP in nanodisc

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