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- EMDB-53924: Primed-state RyR1 in 0.01% POPC micelles, in complex with a nanob... -

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Basic information

Entry
Database: EMDB / ID: EMD-53924
TitlePrimed-state RyR1 in 0.01% POPC micelles, in complex with a nanobody and FKBP12
Map data
Sample
  • Complex: Ryanodine receptor 1 complex with nanobody and FKBP12
    • Protein or peptide: Nanobody 9657
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: Ryanodine receptor 1
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CAFFEINE
  • Ligand: CALCIUM ION
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
KeywordsIon channel / Ca2+ / tetramer / TRANSPORT PROTEIN
Function / homology
Function and homology information


ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine / skin development / organelle membrane / intracellularly gated calcium channel activity ...ATP-gated ion channel activity / terminal cisterna / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cellular response to caffeine / skin development / organelle membrane / intracellularly gated calcium channel activity / smooth endoplasmic reticulum / outflow tract morphogenesis / regulation of ryanodine-sensitive calcium-release channel activity / toxic substance binding / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / striated muscle contraction / voltage-gated calcium channel activity / skeletal muscle fiber development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / muscle contraction / cellular response to calcium ion / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / sarcolemma / calcium ion transmembrane transport / calcium channel activity / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / intracellular membrane-bounded organelle / calcium ion binding / ATP binding / identical protein binding / membrane
Similarity search - Function
Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain ...Ryanodine receptor, SPRY domain 2 / : / Ryanodine receptor junctional solenoid repeat / Ryanodine Receptor TM 4-6 / Ryanodine receptor / Ryanodine receptor, SPRY domain 1 / Ryanodine receptor, SPRY domain 3 / Ryanodine Receptor TM 4-6 / Ryanodine receptor Ryr / RyR domain / : / RyR/IP3 receptor binding core, RIH domain superfamily / RyR/IP3R Homology associated domain / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / RyR and IP3R Homology associated / Inositol 1,4,5-trisphosphate/ryanodine receptor / RIH domain / : / MIR motif / MIR domain / MIR domain profile. / Domain in ryanodine and inositol trisphosphate receptors and protein O-mannosyltransferases / Mir domain superfamily / SPRY domain / B30.2/SPRY domain / B30.2/SPRY domain profile. / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / SPRY domain / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / Ion transport domain / Ion transport protein / EF-hand domain pair / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Ryanodine receptor 1 / Peptidyl-prolyl cis-trans isomerase FKBP1B
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsLi C / Efremov RG
Funding support Belgium, European Union, 3 items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0H5916N Belgium
Research Foundation - Flanders (FWO)G054617N Belgium
European Research Council (ERC)726436European Union
CitationJournal: To Be Published
Title: Primed-state RyR1 in 0.01% POPC micelles, in complex with a nanobody and FKBP
Authors: Li C / Efremov RG
History
DepositionMay 30, 2025-
Header (metadata) releaseSep 17, 2025-
Map releaseSep 17, 2025-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53924.png

Downloads & links

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Map

FileDownload / File: emd_53924.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.45 Å/pix.
x 336 pix.
= 488.544 Å		1.45 Å/pix.
x 336 pix.
= 488.544 Å		1.45 Å/pix.
x 336 pix.
= 488.544 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.454 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.6718214 - 3.786939
Average (Standard dev.)0.0071107647 (±0.11338942)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 488.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : Ryanodine receptor 1 complex with nanobody and FKBP12

EntireName: Ryanodine receptor 1 complex with nanobody and FKBP12
Components
  • Complex: Ryanodine receptor 1 complex with nanobody and FKBP12
    • Protein or peptide: Nanobody 9657
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: Ryanodine receptor 1
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CAFFEINE
  • Ligand: CALCIUM ION
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate

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Supramolecule #1: Ryanodine receptor 1 complex with nanobody and FKBP12

SupramoleculeName: Ryanodine receptor 1 complex with nanobody and FKBP12 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Oryctolagus cuniculus (rabbit)

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Macromolecule #1: Nanobody 9657

MacromoleculeName: Nanobody 9657 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 13.783114 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
QVQLQESGGG LMQAGGSLRL SCTASGSIFS INSMGWYRQA PGKQRELVAT ITSGNSINYA DSVKGRFTIS RDNAKNTVYL QMNSLKPED TAVYYCNADR VPNGYNPWGT PNDEYDYWGQ GTQVTVS

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Macromolecule #2: Peptidyl-prolyl cis-trans isomerase FKBP1B

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 11.667305 KDa
SequenceString:
GVEIETISPG DGRTFPKKGQ TCVVHYTGML QNGKKFDSSR DRNKPFKFRI GKQEVIKGFE EGAAQMSLGQ RAKLTCTPDV AYGATGHPG VIPPNATLIF DVELLNLE

UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B

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Macromolecule #3: Ryanodine receptor 1

MacromoleculeName: Ryanodine receptor 1 / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 564.93175 KDa
SequenceString: VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAGV ESSQGGGHR TLLYGHAILL RHAHSRMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT MHPASKQRSE GEKVRVGDDL I LVSVSSER ...String:
VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAGV ESSQGGGHR TLLYGHAILL RHAHSRMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT MHPASKQRSE GEKVRVGDDL I LVSVSSER YLHLSTASGE LQVDASFMQT LWNMNPICSC CEEGYVTGGH VLRLFHGHMD ECLTISAADS DDQRRLVYYE GG AVCTHAR SLWRLEPLRI SWSGSHLRWG QPLRIRHVTT GRYLALTEDQ GLVVVDACKA HTKATSFCFR VSKEKLDTAP KRD VEGMGP PEIKYGESLC FVQHVASGLW LTYAAPDPKA LRLGVLKKKA ILHQEGHMDD ALFLTRCQQE ESQAARMIHS TAGL YNQFI KGLDSFSGKP RGSGPPAGPA LPIEAVILSL QDLIGYFEPP SEELQHEEKQ SKLRSLRNRQ SLFQEEGMLS LVLNC IDRL NVYTTAAHFA EYAGEEAAES WKEIVNLLYE LLASLIRGNR ANCALFSTNL DWVVSKLDRL EASSGILEVL YCVLIE SPE VLNIIQENHI KSIISLLDKH GRNHKVLDVL CSLCVCNGVA VRSNQDLITE NLLPGRELLL QTNLINYVTS IRPNIFV GR AEGSTQYGKW YFEVMVDEVV PFLTAQATHL RVGWALTEGY SPYPGGGEGW GGNGVGDDLY SYGFDGLHLW TGHVARPV T SPGQHLLAPE DVVSCCLDLS VPSISFRING CPVQGVFEAF NLDGLFFPVV SFSAGVKVRF LLGGRHGEFK FLPPPGYAP CHEAVLPRER LRLEPIKEYR REGPRGPHLV GPSRCLSHTD FVPCPVDTVQ IVLPPHLERI REKLAENIHE LWALTRIEQG WTYGPVRDD NKRLHPCLVN FHSLPEPERN YNLQMSGETL KTLLALGCHV GMADEKAEDN LKKTKLPKTY MMSNGYKPAP L DLSHVRLT PAQTTLVDRL AENGHNVWAR DRVAQGWSYS AVQDIPARRN PRLVPYRLLD EATKRSNRDS LCQAVRTLLG YG YNIEPPD QEPSQVENQS RWDRVRIFRA EKSYTVQSGR WYFEFEAVTT GEMRVGWARP ELRPDVELGA DELAYVFNGH RGQ RWHLGS EPFGRPWQSG DVVGCMIDLT ENTIIFTLNG EVLMSDSGSE TAFREIEIGD GFLPVCSLGP GQVGHLNLGQ DVSS LRFFA ICGLQEGFEP FAINMQRPVT TWFSKSLPQF EPVPPEHPHY EVARMDGTVD TPPCLRLAHR TWGSQNSLVE MLFLR LSLP VQFHQHFRCT AGATPLAPPG LQPPAEDEAR AAEPDPDYEN LRRSAGGWGE AEGGKEGTAK EGTPGGTPQP GVEAQP VRA ENEKDATTEK NKKRGFLFKA KKAAMMTQPP ATPALPRLPH DVVPADNRDD PEIILNTTTY YYSVRVFAGQ EPSCVWV GW VTPDYHQHDM NFDLSKVRAV TVTMGDEQGN VHSSLKCSNC YMVWGGDFVS PGQQGRISHT DLVIGCLVDL ATGLMTFT A NGKESNTFFQ VEPNTKLFPA VFVLPTHQNV IQFELGKQKN IMPLSAAMFL SERKNPAPQC PPRLEVQMLM PVSWSRMPN HFLQVETRRA GERLGWAVQC QDPLTMMALH IPEENRCMDI LELSERLDLQ RFHSHTLRLY RAVCALGNNR VAHALCSHVD QAQLLHALE DAHLPGPLRA GYYDLLISIH LESACRSRRS MLSEYIVPLT PETRAITLFP PGRKGGNARR HGLPGVGVTT S LRPPHHFS PPCFVAALPA AGVAEAPARL SPAIPLEALR DKALRMLGEA VRDGGQHARD PVGGSVEFQF VPVLKLVSTL LV MGIFGDE DVKQILKMIE PEVFTEEEEE EEEEEEEEEE EEEDEEEKEE DEEEEEKEDA EKEEEEAPEG EKEDLEEGLL QMK LPESVK LQMCNLLEYF CDQELQHRVE SLAAFAERYV DKLQANQRSR YALLMRAFTM SAAETARRTR EFRSPPQEQI NMLL HFKDE ADEEDCPLPE DIRQDLQDFH QDLLAHCGIQ LEGEEEEPEE ETSLSSRLRS LLETVRLVKK KEEKPEEELP AEEKK PQSL QELVSHMVVR WAQEDYVQSP ELVRAMFSLL HRQYDGLGEL LRALPRAYTI SPSSVEDTMS LLECLGQIRS LLIVQM GPQ EENLMIQSIG NIMNNKVFYQ HPNLMRALGM HETVMEVMVN VLGGGETKEI RFPKMVTSCC RFLCYFCRIS RQNQRSM FD HLSYLLENSG IGLGMQGSTP LDVAAASVID NNELALALQE QDLEKVVSYL AGCGLQSCPM LLAKGYPDIG WNPCGGER Y LDFLRFAVFV NGESVEENAN VVVRLLIRKP ECFGPALRGE GGSGLLAAIE EAIRISEDPA RDGPGVRRDR RREHFGEEP PEENRVHLGH AIMSFYAALI DLLGRCAPEM HLIQAGKGEA LRIRAILRSL VPLDDLVGII SLPLQIPTLG KDGALVQPKM SASFVPDHK ASMVLFLDRV YGIENQDFLL HVLDVGFLPD MRAAASLDTA TFSTTEMALA LNRYLCLAVL PLITKCAPLF A GTEHRAIM VDSMLHTVYR LSRGRSLTKA QRDVIEDCLM ALCRYIRPSM LQHLLRRLVF DVPILNEFAK MPLKLLTNHY ER CWKYYCL PTGWANFGVT SEEELHLTRK LFWGIFDSLA HKKYDQELYR MAMPCLCAIA GALPPDYVDA SYSSKAEKKA TVD AEGNFD PRPVETLNVI IPEKLDSFIN KFAEYTHEKW AFDKIQNNWS YGENVDEELK THPMLRPYKT FSEKDKEIYR WPIK ESLKA MIAWEWTIEK AREGEEERTE KKKTRKISQT AQTYDPREGY NPQPPDLSGV TLSRELQAMA EQLAENYHNT WGRKK KQEL EAKGGGTHPL LVPYDTLTAK EKARDREKAQ ELLKFLQMNG YAVTRGLKDM ELDTSSIEKR FAFGFLQQLL RWMDIS QEF IAHLEAVVSS GRVEKSPHEQ EIKFFAKILL PLINQYFTNH CLYFLSTPAK VLGSGGHASN KEKEMITSLF CKLAALV RH RVSLFGTDAP AVVNCLHILA RSLDARTVMK SGPEIVKAGL RSFFESASED IEKMVENLRL GKVSQARTQV KGVGQNLT Y TTVALLPVLT TLFQHIAQHQ FGDDVILDDV QVSCYRTLCS IYSLGTTKNT YVEKLRPALG ECLARLAAAM PVAFLEPQL NEYNACSVYT TKSPRERAIL GLPNSVEEMC PDIPVLDRLM ADIGGLAESG ARYTEMPHVI EITLPMLCSY LPRWWERGPE APPPALPAG APPPCTAVTS DHLNSLLGNI LRIIVNNLGI DEATWMKRLA VFAQPIVSRA RPELLHSHFI PTIGRLRKRA G KVVAEEEQ LRLEAKAEAE EGELLVRDEF SVLCRDLYAL YPLLIRYVDN NRAHWLTEPN ANAEELFRMV GEIFIYWSKS HN FKREEQN FVVQNEINNM SFLTADSKSK MAKAGDAQSG GSDQERTKKK RRGDRYSVQT SLIVATLKKM LPIGLNMCAP TDQ DLIMLA KTRYALKDTD EEVREFLQNN LHLQGKVEGS PSLRWQMALY RGLPGREEDA DDPEKIVRRV QEVSAVLYHL EQTE HPYKS KKAVWHKLLS KQRRRAVVAC FRMTPLYNLP THRACNMFLE SYKAAWILTE DHSFEDRMID DLSKAGEQEE EEEEV EEKK PDPLHQLVLH FSRTALTEKS KLDEDYLYMA YADIMAKSCH LEEGGENGEA EEEEVEVSFE EKEMEKQRLL YQQSRL HTR GAAEMVLQMI SACKGETGAM VSSTLKLGIS ILNGGNAEVQ QKMLDYLKDK KEVGFFQSIQ ALMQTCSVLD LNAFERQ NK AEGLGMVNED GTVINRQNGE KVMADDEFTQ DLFRFLQLLC EGHNNDFQNY LRTQTGNTTT INIIICTVDY LLRLQESI S DFYWYYSGKD VIEEQGKRNF SKAMSVAKQV FNSLTEYIQG PCTGNQQSLA HSRLWDAVVG FLHVFAHMMM KLAQDSSQI ELLKELLDLQ KDMVVMLLSL LEGNVVNGMI ARQMVDMLVE SSSNVEMILK FFDMFLKLKD IVGSEAFQDY VTDPRGLISK KDFQKAMDS QKQFTGPEIQ FLLSCSEADE NEMINFEEFA NRFQEPARDI GFNVAVLLTN LSEHVPHDPR LRNFLELAES I LEYFRPYL GRIEIMGASR RIERIYFEIS ETNRAQWEMP QVKESKRQFI FDVVNEGGEA EKMELFVSFC EDTIFEMQIA AQ ISEPEGE PEADEDEGMG EAAAEGAEEG AAGAEGAAGT VAAGATARLA AAAARALRGL SYRSLRRRVR RLRRLTAREA ATA LAALLW AVVARAGAAG AGAAAGALRL LWGSLFGGGL VEGAKKVTVT ELLAGMPDPT SDEVHGEQPA GPGGDADGAG EGEG EGDAA EGDGDEEVAG HEAGPGGAEG VVAVADGGPF RPEGAGGLGD MGDTTPAEPP TPEGSPILKR KLGVDGEEEE LVPEP EPEP EPEPEKADEE NGEKEEVPEA PPEPPKKAPP SPPAKKEEAG GAGMEFWGEL EVQRVKFLNY LSRNFYTLRF LALFLA FAI NFILLFYKVS DSPPGEDDME GSAAGDLAGA GSGGGSGWGS GAGEEAEGDE DENMVYYFLE ESTGYMEPAL WCLSLLH TL VAFLCIIGYN CLKVPLVIFK REKELARKLE FDGLYITEQP GDDDVKGQWD RLVLNTPSFP SNYWDKFVKR KVLDKHGD I FGRERIAELL GMDLASLEIT AHNERKPDPP PGLLTWLMSI DVKYQIWKFG VIFTDNSFLY LGWYMVMSLL GHYNNFFFA AHLLDIAMGV KTLRTILSSV THNGKQLVMT VGLLAVVVYL YTVVAFNFFR KFYNKSEDED EPDMKCDDMM TCYLFHMYVG VRAGGGIGD EIEDPAGDEY ELYRVVFDIT FFFFVIVILL AIIQGLIIDA FGELRDQQEQ VKEDMETKCF ICGIGSDYFD T TPHGFETH TLEEHNLANY MFFLMYLINK DETEHTGQES YVWKMYQERC WDFFPAGDCF RKQYEDQLS

UniProtKB: Ryanodine receptor 1

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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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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #6: CAFFEINE

MacromoleculeName: CAFFEINE / type: ligand / ID: 6 / Number of copies: 4 / Formula: CFF
Molecular weightTheoretical: 194.191 Da
Chemical component information

ChemComp-CFF:
CAFFEINE / medication*YM

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Macromolecule #7: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 4 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #8: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 8 / Number of copies: 24 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

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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

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Sample stageSpecimen holder model: JEOL CRYOSPECPORTER

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8rrw

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39983
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 8

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