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- EMDB-23692: High resolution structure of the membrane embedded skeletal muscl... -

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Basic information

Entry
Database: EMDB / ID: EMD-23692
TitleHigh resolution structure of the membrane embedded skeletal muscle ryanodine receptor
Map data
Sample
  • Complex: Proteoliposomal ryanodine receptor with calstabin-2
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: Ryanodine receptor 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CALCIUM IONCalcium
  • Ligand: ZINC ION
  • Ligand: CAFFEINE
Function / homology
Function and homology information


ATP-gated ion channel activity / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of release of sequestered calcium ion into cytosol / terminal cisterna / negative regulation of insulin secretion involved in cellular response to glucose stimulus / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus ...ATP-gated ion channel activity / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of release of sequestered calcium ion into cytosol / terminal cisterna / negative regulation of insulin secretion involved in cellular response to glucose stimulus / ryanodine receptor complex / ryanodine-sensitive calcium-release channel activity / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / ossification involved in bone maturation / cell communication by electrical coupling involved in cardiac conduction / response to redox state / protein maturation by protein folding / 'de novo' protein folding / skin development / negative regulation of heart rate / negative regulation of phosphoprotein phosphatase activity / FK506 binding / positive regulation of axon regeneration / cellular response to caffeine / intracellularly gated calcium channel activity / outflow tract morphogenesis / organelle membrane / calcium-mediated signaling using intracellular calcium source / toxic substance binding / smooth muscle contraction / negative regulation of ryanodine-sensitive calcium-release channel activity / voltage-gated calcium channel activity / response to vitamin E / calcium channel inhibitor activity / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / skeletal muscle fiber development / protein peptidyl-prolyl isomerization / T cell proliferation / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / release of sequestered calcium ion into cytosol / regulation of ryanodine-sensitive calcium-release channel activity / Ion homeostasis / sarcoplasmic reticulum membrane / calcium channel complex / regulation of cytosolic calcium ion concentration / cellular response to calcium ion / muscle contraction / sarcoplasmic reticulum / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium ion transmembrane transport / calcium channel activity / response to hydrogen peroxide / intracellular calcium ion homeostasis / Stimuli-sensing channels / Z disc / disordered domain specific binding / positive regulation of cytosolic calcium ion concentration / protein refolding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / signaling receptor binding / calcium ion binding / ATP binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / Ryanodine receptor junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / 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 junctional solenoid repeat / Ryanodine receptor, SPRY domain 2 / 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. / SPRY domain / B30.2/SPRY domain superfamily / Domain in SPla and the RYanodine Receptor. / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / 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) / Homo sapiens (human) / Rabbit (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsMelville Z / Kim K / Clarke OB / Marks AR
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL145473 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01DK118240 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL142903 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL140934 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01AR070194 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)T32 HL120826 United States
CitationJournal: Structure / Year: 2022
Title: High-resolution structure of the membrane-embedded skeletal muscle ryanodine receptor.
Authors: Zephan Melville / Kookjoo Kim / Oliver B Clarke / Andrew R Marks /
Abstract: The type 1 ryanodine receptor (RyR)/calcium release channel on the sarcoplasmic reticulum (SR) is required for skeletal muscle excitation-contraction coupling and is the largest known ion channel, ...The type 1 ryanodine receptor (RyR)/calcium release channel on the sarcoplasmic reticulum (SR) is required for skeletal muscle excitation-contraction coupling and is the largest known ion channel, composed of four 565-kDa protomers. Cryogenic electron microscopy (cryo-EM) studies of the RyR have primarily used detergent to solubilize the channel; in the present study, we have used cryo-EM to solve high-resolution structures of the channel in liposomes using a gel-filtration approach with on-column detergent removal to form liposomes and incorporate the channel simultaneously. This allowed us to resolve the structure of the channel in the primed and open states at 3.4 and 4.0 Å, respectively, with a single dataset. This method offers validation for detergent-based structures of the RyR and offers a starting point for utilizing a chemical gradient mimicking the SR, where Ca concentrations are millimolar in the lumen and nanomolar in the cytosol.
History
DepositionMar 25, 2021-
Header (metadata) releaseSep 8, 2021-
Map releaseSep 8, 2021-
UpdateJan 19, 2022-
Current statusJan 19, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.121
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.121
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7m6a
  • Surface level: 0.121
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_23692.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.831 Å
Density
Contour LevelBy AUTHOR: 0.121 / Movie #1: 0.121
Minimum - Maximum-0.032410763 - 1.1190653
Average (Standard dev.)0.016048985 (±0.031090688)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 425.472 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8310.8310.831
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z425.472425.472425.472
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0321.1190.016

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Supplemental data

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Mask #1

Fileemd_23692_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #2

Fileemd_23692_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_23692_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire : Proteoliposomal ryanodine receptor with calstabin-2

EntireName: Proteoliposomal ryanodine receptor with calstabin-2
Components
  • Complex: Proteoliposomal ryanodine receptor with calstabin-2
    • Protein or peptide: Peptidyl-prolyl cis-trans isomerase FKBP1B
    • Protein or peptide: Ryanodine receptor 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: CALCIUM IONCalcium
  • Ligand: ZINC ION
  • Ligand: CAFFEINE

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Supramolecule #1: Proteoliposomal ryanodine receptor with calstabin-2

SupramoleculeName: Proteoliposomal ryanodine receptor with calstabin-2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
Molecular weightTheoretical: 2.31 MDa

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Macromolecule #1: Peptidyl-prolyl cis-trans isomerase FKBP1B

MacromoleculeName: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.798501 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGVEIETISP GDGRTFPKKG QTCVVHYTGM LQNGKKFDSS RDRNKPFKFR IGKQEVIKGF EEGAAQMSLG QRAKLTCTPD VAYGATGHP GVIPPNATLI FDVELLNLE

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Macromolecule #2: Ryanodine receptor 1

MacromoleculeName: Ryanodine receptor 1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rabbit (rabbit)
Molecular weightTheoretical: 565.908625 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 TWGSQ NSLV EMLFLRLSLP VQFHQHFRCT AGATPLAPPG LQPPAEDEAR AAEPDPDYEN LRRSAGGWGE AEGGKEGTAK EGTPGG TPQ PGVEAQPVRA ENEKDATTEK NKKRGFLFKA KKAAMMTQPP ATPALPRLPH DVVPADNRDD PEIILNTTTY YYSVRVF AG QEPSCVWVGW VTPDYHQHDM NFDLSKVRAV TVTMGDEQGN VHSSLKCSNC YMVWGGDFVS PGQQGRISHT DLVIGCLV D LATGLMTFTA NGKESNTFFQ VEPNTKLFPA VFVLPTHQNV IQFELGKQKN IMPLSAAMFL SERKNPAPQC PPRLEVQML MPVSWSRMPN HFLQVETRRA GERLGWAVQC QDPLTMMALH IPEENRCMDI LELSERLDLQ RFHSHTLRLY RAVCALGNNR VAHALCSHV DQAQLLHALE DAHLPGPLRA GYYDLLISIH LESACRSRRS MLSEYIVPLT PETRAITLFP PGRKGGNARR H GLPGVGVT TSLRPPHHFS PPCFVAALPA AGVAEAPARL SPAIPLEALR DKALRMLGEA VRDGGQHARD PVGGSVEFQF VP VLKLVST LLVMGIFGDE DVKQILKMIE PEVFTEEEEE EEEEEEEEEE EEEDEEEKEE DEEEEEKEDA EKEEEEAPEG EKE DLEEGL LQMKLPESVK LQMCNLLEYF CDQELQHRVE SLAAFAERYV DKLQANQRSR YALLMRAFTM SAAETARRTR EFRS PPQEQ INMLLHFKDE ADEEDCPLPE DIRQDLQDFH QDLLAHCGIQ LEGEEEEPEE ETSLSSRLRS LLETVRLVKK KEEKP EEEL PAEEKKPQSL QELVSHMVVR WAQEDYVQSP ELVRAMFSLL HRQYDGLGEL LRALPRAYTI SPSSVEDTMS LLECLG QIR SLLIVQMGPQ EENLMIQSIG NIMNNKVFYQ HPNLMRALGM HETVMEVMVN VLGGGETKEI RFPKMVTSCC RFLCYFC RI SRQNQRSMFD HLSYLLENSG IGLGMQGSTP LDVAAASVID NNELALALQE QDLEKVVSYL AGCGLQSCPM LLAKGYPD I GWNPCGGERY LDFLRFAVFV NGESVEENAN VVVRLLIRKP ECFGPALRGE GGSGLLAAIE EAIRISEDPA RDGPGVRRD RRREHFGEEP PEENRVHLGH AIMSFYAALI DLLGRCAPEM HLIQAGKGEA LRIRAILRSL VPLDDLVGII SLPLQIPTLG KDGALVQPK MSASFVPDHK ASMVLFLDRV YGIENQDFLL HVLDVGFLPD MRAAASLDTA TFSTTEMALA LNRYLCLAVL P LITKCAPL FAGTEHRAIM VDSMLHTVYR LSRGRSLTKA QRDVIEDCLM ALCRYIRPSM LQHLLRRLVF DVPILNEFAK MP LKLLTNH YERCWKYYCL PTGWANFGVT SEEELHLTRK LFWGIFDSLA HKKYDQELYR MAMPCLCAIA GALPPDYVDA SYS SKAEKK ATVDAEGNFD PRPVETLNVI IPEKLDSFIN KFAEYTHEKW AFDKIQNNWS YGENVDEELK THPMLRPYKT FSEK DKEIY RWPIKESLKA MIAWEWTIEK AREGEEERTE KKKTRKISQT AQTYDPREGY NPQPPDLSGV TLSRELQAMA EQLAE NYHN TWGRKKKQEL EAKGGGTHPL LVPYDTLTAK EKARDREKAQ ELLKFLQMNG YAVTRGLKDM ELDTSSIEKR FAFGFL QQL LRWMDISQEF IAHLEAVVSS GRVEKSPHEQ EIKFFAKILL PLINQYFTNH CLYFLSTPAK VLGSGGHASN KEKEMIT SL FCKLAALVRH RVSLFGTDAP AVVNCLHILA RSLDARTVMK SGPEIVKAGL RSFFESASED IEKMVENLRL GKVSQART Q VKGVGQNLTY TTVALLPVLT TLFQHIAQHQ FGDDVILDDV QVSCYRTLCS IYSLGTTKNT YVEKLRPALG ECLARLAAA MPVAFLEPQL NEYNACSVYT TKSPRERAIL GLPNSVEEMC PDIPVLDRLM ADIGGLAESG ARYTEMPHVI EITLPMLCSY LPRWWERGP EAPPPALPAG APPPCTAVTS DHLNSLLGNI LRIIVNNLGI DEATWMKRLA VFAQPIVSRA RPELLHSHFI P TIGRLRKR AGKVVAEEEQ LRLEAKAEAE EGELLVRDEF SVLCRDLYAL YPLLIRYVDN NRAHWLTEPN ANAEELFRMV GE IFIYWSK SHNFKREEQN FVVQNEINNM SFLTADSKSK MAKAGDAQSG GSDQERTKKK RRGDRYSVQT SLIVATLKKM LPI GLNMCA PTDQDLIMLA KTRYALKDTD EEVREFLQNN LHLQGKVEGS PSLRWQMALY RGLPGREEDA DDPEKIVRRV QEVS AVLYH LEQTEHPYKS KKAVWHKLLS KQRRRAVVAC FRMTPLYNLP THRACNMFLE SYKAAWILTE DHSFEDRMID DLSKA GEQE EEEEEVEEKK PDPLHQLVLH FSRTALTEKS KLDEDYLYMA YADIMAKSCH LEEGGENGEA EEEEVEVSFE EKEMEK QRL LYQQSRLHTR GAAEMVLQMI SACKGETGAM VSSTLKLGIS ILNGGNAEVQ QKMLDYLKDK KEVGFFQSIQ ALMQTCS VL DLNAFERQNK AEGLGMVNED GTVINRQNGE KVMADDEFTQ DLFRFLQLLC EGHNNDFQNY LRTQTGNTTT INIIICTV D YLLRLQESIS DFYWYYSGKD VIEEQGKRNF SKAMSVAKQV FNSLTEYIQG PCTGNQQSLA HSRLWDAVVG FLHVFAHMM MKLAQDSSQI ELLKELLDLQ KDMVVMLLSL LEGNVVNGMI ARQMVDMLVE SSSNVEMILK FFDMFLKLKD IVGSEAFQDY VTDPRGLIS KKDFQKAMDS QKQFTGPEIQ FLLSCSEADE NEMINFEEFA NRFQEPARDI GFNVAVLLTN LSEHVPHDPR L RNFLELAE SILEYFRPYL GRIEIMGASR RIERIYFEIS ETNRAQWEMP QVKESKRQFI FDVVNEGGEA EKMELFVSFC ED TIFEMQI AAQISEPEGE PEADEDEGMG EAAAEGAEEG AAGAEGAAGT VAAGATARLA AAAARALRGL SYRSLRRRVR RLR RLTARE AATALAALLW AVVARAGAAG AGAAAGALRL LWGSLFGGGL VEGAKKVTVT ELLAGMPDPT SDEVHGEQPA GPGG DADGA GEGEGEGDAA EGDGDEEVAG HEAGPGGAEG VVAVADGGPF RPEGAGGLGD MGDTTPAEPP TPEGSPILKR KLGVD GEEE ELVPEPEPEP EPEPEKADEE NGEKEEVPEA PPEPPKKAPP SPPAKKEEAG GAGMEFWGEL EVQRVKFLNY LSRNFY TLR FLALFLAFAI NFILLFYKVS DSPPGEDDME GSAAGDLAGA GSGGGSGWGS GAGEEAEGDE DENMVYYFLE ESTGYME PA LWCLSLLHTL VAFLCIIGYN CLKVPLVIFK REKELARKLE FDGLYITEQP GDDDVKGQWD RLVLNTPSFP SNYWDKFV K RKVLDKHGDI FGRERIAELL GMDLASLEIT AHNERKPDPP PGLLTWLMSI DVKYQIWKFG VIFTDNSFLY LGWYMVMSL LGHYNNFFFA AHLLDIAMGV KTLRTILSSV THNGKQLVMT VGLLAVVVYL YTVVAFNFFR KFYNKSEDED EPDMKCDDMM TCYLFHMYV GVRAGGGIGD EIEDPAGDEY ELYRVVFDIT FFFFVIVILL AIIQGLIIDA FGELRDQQEQ VKEDMETKCF I CGIGSDYF DTTPHGFETH TLEEHNLANY MFFLMYLINK DETEHTGQES YVWKMYQERC WDFFPAGDCF RKQYEDQLS

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #4: CALCIUM ION

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

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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 / Caffeine (data page)

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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

Concentration3 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormula
10.0 mMHEPES
150.0 mMNaClSodium chloride
0.5 mMTCEP
1.0 mMEGTA
Sugar embeddingMaterial: Lipid
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11187 / Average exposure time: 2.5 sec. / Average electron dose: 58.34 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2000000
CTF correctionSoftware - Name: cryoSPARC (ver. 2)
Startup modelType of model: INSILICO MODEL / In silico model: cryoSPARC ab initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2) / Details: cryoSPARC branch-and-bound
Final 3D classificationNumber classes: 100 / Avg.num./class: 872 / Software - Name: cryoSPARC (ver. 2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 2) / Details: cryoSPARC branch-and-bound
Final reconstructionNumber classes used: 41 / Applied symmetry - Point group: C4 (4 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 53882
FSC plot (resolution estimation)

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