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- EMDB-22615: Cryo-EM structure of rabbit RyR1 in the presence of Mg2+ and AMP-... -

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Basic information

Entry
Database: EMDB / ID: EMD-22615
TitleCryo-EM structure of rabbit RyR1 in the presence of Mg2+ and AMP-PCP in nanodisc
Map dataPost-processed full map
Sample
  • Complex: Rabbit RyR1 with Mg2+ and AMP-PCP
    • Protein or peptide: RyR1Ryanodine receptor 1
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
KeywordsRyanodine Receptor / RyR1 / Intracellular Calcium channel / Mg2+ / Inhibition / Excitation-Contraction coupling / TRANSPORT PROTEIN
Biological speciesOryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 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: Nat Commun / Year: 2024
Title: Interplay between Mg2+ and Ca2+ at multiple sites of the ryanodine receptor
Authors: Nayak AR / Rangubpit W / Will AH / Hu Y / Castro-Hartmann P / Lobo JJ / Dryden K / Lamb GD / Sompornpisut P / Samso M
History
DepositionSep 5, 2020-
Header (metadata) releaseSep 22, 2021-
Map releaseSep 22, 2021-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing 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
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7k0s
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22615.png

Downloads & links

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Map

FileDownload / File: emd_22615.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPost-processed full map
Voxel sizeX=Y=Z: 1.36 Å
Density
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.025
Minimum - Maximum-0.12640421 - 0.20036845
Average (Standard dev.)0.0010575 (±0.0070624556)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 478.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.361.361.36
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z478.720478.720478.720
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-0.1260.2000.001

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Supplemental data

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Mask #1

Fileemd_22615_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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

Fileemd_22615_additional_1.map
AnnotationUnfiltered and unmasked half map1 up to Nyquist frequency
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unfiltered and unmasked half map2 up to Nyquist frequency

Fileemd_22615_additional_2.map
AnnotationUnfiltered and unmasked half map2 up to Nyquist frequency
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Masked half map1

Fileemd_22615_half_map_1.map
AnnotationMasked half map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Masked half map2

Fileemd_22615_half_map_2.map
AnnotationMasked half map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Rabbit RyR1 with Mg2+ and AMP-PCP

EntireName: Rabbit RyR1 with Mg2+ and AMP-PCP
Components
  • Complex: Rabbit RyR1 with Mg2+ and AMP-PCP
    • Protein or peptide: RyR1Ryanodine receptor 1
  • Ligand: PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Rabbit RyR1 with Mg2+ and AMP-PCP

SupramoleculeName: Rabbit RyR1 with Mg2+ and AMP-PCP / type: complex / 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 weightTheoretical: 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: Oryctolagus cuniculus (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) 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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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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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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 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

Concentration4.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationNameFormula
20.0 mMMOPS (pH7.4)
635.0 mMPotassium ChlorideKCl
2.0 mMDithiothreitol
5.0 mMAMP-PCP
5.0 mMMagnesium ChlorideMgCl2
2.0 mMEGTA
GridModel: C-flat-2/1 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / 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: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
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: 2 / Number real images: 3371 / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 115741
Startup modelType of model: EMDB MAP
EMDB ID:

8391

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 1.4)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 68155
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7k0s:
Cryo-EM structure of rabbit RyR1 in the presence of Mg2+ and AMP-PCP in nanodisc

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