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Yorodumi- EMDB-70599: Cryo-EM Structure of Pig Ryanodine Receptor 1 R615C Mutant: Drug ... -
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Open data
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Basic information
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| Title | Cryo-EM Structure of Pig Ryanodine Receptor 1 R615C Mutant: Drug Bound Open Conformation Consensus Map | |||||||||
Map data | Consensus Map | |||||||||
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Keywords | Ion Channel / Calcium Channel / TRANSPORT PROTEIN | |||||||||
| Function / homology | Function and homology informationpositive regulation of sequestering of calcium ion / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / negative regulation of release of sequestered calcium ion into cytosol / insulin secretion involved in cellular response to glucose stimulus / terminal cisterna / ryanodine-sensitive calcium-release channel activity / ryanodine receptor complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum ...positive regulation of sequestering of calcium ion / negative regulation of calcium-mediated signaling / negative regulation of insulin secretion involved in cellular response to glucose stimulus / neuronal action potential propagation / negative regulation of release of sequestered calcium ion into cytosol / insulin secretion involved in cellular response to glucose stimulus / terminal cisterna / ryanodine-sensitive calcium-release channel activity / ryanodine receptor complex / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / response to redox state / ossification involved in bone maturation / negative regulation of heart rate / cellular response to caffeine / 'de novo' protein folding / skin development / FK506 binding / organelle membrane / smooth endoplasmic reticulum / outflow tract morphogenesis / smooth muscle contraction / T cell proliferation / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / voltage-gated calcium channel activity / calcium channel inhibitor activity / skeletal muscle fiber development / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / Ion homeostasis / release of sequestered calcium ion into cytosol / calcium channel complex / sarcoplasmic reticulum membrane / cellular response to calcium ion / muscle contraction / sarcoplasmic reticulum / protein maturation / calcium channel regulator activity / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium-mediated signaling / sarcolemma / calcium ion transmembrane transport / Stimuli-sensing channels / calcium channel activity / Z disc / intracellular calcium ion homeostasis / 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 / cytoplasm Similarity search - Function | |||||||||
| Biological species | ![]() Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.36 Å | |||||||||
Authors | Molinarolo SM / Van Petegem F | |||||||||
| Funding support | Canada, 1 items
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Citation | Journal: Nat Commun / Year: 2025Title: Cryo-electron microscopy reveals sequential binding and activation of Ryanodine Receptors by statin triplets. Authors: Steven Molinarolo / Carmen R Valdivia / Héctor H Valdivia / Filip Van Petegem / ![]() Abstract: Statins are the most prescribed class of drugs and inhibit a key enzyme in the cholesterol biosynthesis pathway. Many patients have reported mild to severe muscle related symptoms and a subset are at ...Statins are the most prescribed class of drugs and inhibit a key enzyme in the cholesterol biosynthesis pathway. Many patients have reported mild to severe muscle related symptoms and a subset are at risk for rhabdomyolysis. Sequence variants in RyR1, the skeletal muscle Ryanodine Receptor, correlate with intolerance to statins, but whether RyR1 can bind statins directly has remained unclear. Here we report cryo-EM structures of RyR1 in the absence and presence of atorvastatin, firmly establishing RyR1 as an unintended off-target. Our results show an unusual binding mode whereby three atorvastatin molecules bind together in a cleft formed by the pseudo-voltage sensing domain, making extensive interactions with each other and with RyR1. Atorvastatin activates RyR1 in a sequential way, whereby one statin per subunit can bind to the transmembrane region of a closed RyR1, with small structural perturbations that prime the channel for opening. Binding of two additional statins per subunit is associated with a widening of the pseudo-voltage sensing domain that triggers opening of the pore. Comparison with atorvastatin binding to HMG-CoA reductase, its intended target, offers clues on how to modify the statin to reduce RyR1 binding, while leaving binding to HMG-CoA reductase unperturbed. | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_70599.map.gz | 255.2 MB | EMDB map data format | |
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| Header (meta data) | emd-70599-v30.xml emd-70599.xml | 24.7 KB 24.7 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_70599_fsc.xml | 17 KB | Display | FSC data file |
| Images | emd_70599.png | 147.2 KB | ||
| Filedesc metadata | emd-70599.cif.gz | 8.9 KB | ||
| Others | emd_70599_half_map_1.map.gz emd_70599_half_map_2.map.gz | 474.2 MB 474.2 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-70599 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-70599 | HTTPS FTP |
-Validation report
| Summary document | emd_70599_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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| Full document | emd_70599_full_validation.pdf.gz | 1.1 MB | Display | |
| Data in XML | emd_70599_validation.xml.gz | 25.8 KB | Display | |
| Data in CIF | emd_70599_validation.cif.gz | 34 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-70599 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-70599 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9ol6C ![]() 9pwoC C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_70599.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Consensus Map | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.96 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: Consensus Half B
| File | emd_70599_half_map_1.map | ||||||||||||
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| Annotation | Consensus Half B | ||||||||||||
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| Density Histograms |
-Half map: Consensus Half A
| File | emd_70599_half_map_2.map | ||||||||||||
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| Annotation | Consensus Half A | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
-Entire : Ryanodine Receptor 1 and FKBP12.6 complex
| Entire | Name: Ryanodine Receptor 1 and FKBP12.6 complex |
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| Components |
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-Supramolecule #1: Ryanodine Receptor 1 and FKBP12.6 complex
| Supramolecule | Name: Ryanodine Receptor 1 and FKBP12.6 complex / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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| Source (natural) | Organism: ![]() |
| Molecular weight | Theoretical: 2.39 MDa |
-Macromolecule #1: pig Ryanodine Receptor 1 R615C mutant
| Macromolecule | Name: pig Ryanodine Receptor 1 R615C mutant / type: protein_or_peptide / ID: 1 / Details: Pig RyR1 with R615C / Enantiomer: LEVO |
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| Source (natural) | Organism: ![]() |
| Sequence | String: MGDGGEGEDE VQFLRTDDEV VLQCNATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFVL EQSLSVRALQ EMLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSGMYLS C LTTSRSMT DKLAFDVGLQ EDATGEACWW TTHPASKQRS EGEKVRVGDD ...String: MGDGGEGEDE VQFLRTDDEV VLQCNATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFVL EQSLSVRALQ EMLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSGMYLS C LTTSRSMT DKLAFDVGLQ EDATGEACWW TTHPASKQRS EGEKVRVGDD LILVSVSSER YL HLSTASG ELQVDASFMQ TLWNMNPICS GCEEGYVTGG HVLRLFHGHM DECLTISPAD SDD QRRLVY YEGGSVCTHA RSLWRLEPLR ISWSGSHLRW GQPLRIRHVT TGRYLALIED QGLV VVDAS KAHTKATSFC FRISKEKLDT APKRDVEGMG PPEIKYGESL CFVQHVASGL WLTYA APDP KALRLGVLKK KAILHQEGHM DDALSLTRCQ QEESQAARMI YSTAGLYNHF IKGLDS FSG KPRGSGAPAG TALPLEGVIL SLQDLIGYFE PPSEELQHEE KQSKLRSLRN RQSLFQE EG MLSLVLNCID RLNVYTTAAH FAEFAGEEAA ESWKEIVNLL YEILASLIRG NRANCALF S NNLDWLVSKL DRLEASSGIL EVLYCVLIES PEVLNIIQEN HIKSIISLLD KHGRNHKVL DVLCSLCVCN GVAVCSNQDL ITENLLPGRE LLLQTNLINY VTSIRPNIFV GRAEGTTQYS KWYFEVMVD EVVPFLTAQA THLRVGWALT EGYSPYPGGG EGWGGNGVGD DLYSYGFDGL H LWTGHVPR LVTSPGQHLL APEDVVSCCL DLSVPSISFR INGCPVQGVF EAFNLNGLFF PV VSFSAGV KVRFLLGGRH GEFKFLPPPG YAPCHEAVLP RERLRLEPIK EYRREGPRGP HLV GPSRCL SHTDFVPCPV DTVQIVLPPH LERIREKLAE NIHELWALTR IEQGWTYGPV RDDN KRLHP CLVDFHSLPE PERNYNLQMS GETLKTLLAL GCHVGMADEK AEDNLRKTKL PKTYM MSNG YKPAPLDLSH VRLTPAQTTL VDRLAENGHN VWARDRVAQG WSYSAVQDIP ARRNPR LVP YRLLDEATKR SNRDSLCQAV RTLLGYGYNI EPPDQEPSQV ESQSRWDRVR IFRAEKS YA VQSGRWYFEF EAVTTGEMRV GWARPELRPD VELGADELAY VFNGHRGQRW HLGSELFG R PWQSGDVVGC MIDLTENTII FTLNGEVLMS DSGSETAFRD IEVGDGFLPV CSLGPGQVG HLNLGQDVSS LRFFAICGLQ EGFEPFAINM QRPVTTWFSK SLPQFEAVPL EHPHYEVSRV DGTVDTPPC LRLTHRTWGS QNSLVEMLFL RLSLPVQFHQ HFRCTAGATP LAPPGLQPPA E DEARAAEP DPDYENLRRS AGRWGEAEGG KEGTAKEGAP GGTAQAGVEA QPPRAENEKD AT TEKNKKR GFLFKAKKAA MMTQPPATPT LPRLPHEVVP ADDRDDPDII LNTTTYYYSV RVF AGQEPS CVWVGWVTPD YHQHDMNFDL TKVRAVTVTM GDEQGNIHSS LKCSNCYMVW GGDF VSPGQ QGRISHTDLV IGCLVDLATG LMTFTANGKE SNTFFQVEPN TKLFPAVFVL PTHQN VIQF ELGKQKNIMP LSAAMFLSER KNPAPQCPPR LEMQMLMPVS WSRMPNHFLR VETRRA GER LGWAVQCQEP LTMMALHIPE ENRCMDILEL SERLDLQQFH SHTLRLYRAV CALGNNR VA HALCSHVDQA QLLHALEDAH LPGPLRAGYY DLLISIHLES ACRSRRSMLS EYIVPLTP E TRAITLFPPG KRTENGPRRH GLPGVGVTTS LRPPHHFSAP CFVAALPAVG AAEAPARLS PSIPLEALRD KALRMLGEAV RDGGQHARDP VGGSVEFQFV PVLKLVSTLL VMGIFGDEDV KQILKMIEP EVFTEEEEEE EEEEEEEEED EEEKEEDEEE EAREKEDEEK EEEETAEGEK E EYLEEGLL QMKLPESVKL QMCNLLEYFC DQELQHRVES LAAFAERYVD KLQANQRDRY GI LMKAFTM TAAETARRTR EFRSPPQEQI NMLLHFKDGE DEEDCPLPDE IRQDLLEFHQ DLL THCGIQ LEGEEEEPEE EATLGSRLMS LLEKVRLVKK KEEKSEEEPP AEESKAQSLQ ELVS HTVVR WAQEDFVQSP ELVRAMFSLL HRQYDGLGEL LRALPRAYTI SPSSVEDTMS LLECL GQIR SLLIVQMGPQ EENLMIQSIG NIMNNKVFYQ HPNLMRALGM HETVMEVMVN VLGGGE SKE IRFPKMVTSC CRFLCYFCRI SRQNQRSMFD HLSYLLENSG IGLGMQGSTP LDVAAAS VI DNNELALALQ EQDLEKVVSY LAGCGLQSCP MLLAKGYPDI GWNPCGGERY LDFLRFAV F VNGESVEENA NVVVRLLIRK PECFGPALRG EGGSGLLATI EEAIRISEDP ARDGPGVRR DRRREHFGEE PPEENRVHLG HAIMSFYAAL IDLLGRCAPE MHLIQAGKGE ALRIRAILRS LVPLDDLVG IISLPLQIPT LGKDGALVQP KMSASFVPDH KASMVLFLDR VYGIENQDFL L HVLDVGFL PDMRAAASLD TATFSTTEMA LALNRYLCLA VLPLITKCAP LFAGTEHRAI MV DSMLHTV YRLSRGRSLT KAQRDVIEEC LMALCRYIRP SMLQHLLRRL VFDVPILNEF AKM PLKLLT NHYERCWKYY CLPTGWANFG VTSEEELHLT RKLFWGIFDS LAHKKYDPEL YRMA MPCLC AIAGALPPDY VDASYSSKAE KKATVDAEGN FDPRPVETLN VIIPEKLDSF INKFA EYTH EKWAFDKIQN NWSYGENIDE ELKTHPMLRP YKTFSEKDKE IYRWPIKESL KAMIAW EWT IEKAREGEEE KTEKKKTRKI SQSAQTYDAR EGYNPQPPDL SGVTLSRELQ AMAEQLA EN YHNTWGRKKK QELEAKGGGT HPLLVPYDTL TAKEKARDRE KAQELLKFLQ MNGYAVTR G LKDMELDTSS IEKRFAFGFL QQLLRWMDIS QEFIAHLEAV VSSGRVEKSP HEQEIKFFA KILLPLINQY FTNHCLYFLS TPAKVLGSGG HASNKEKEMI TSLFCKLAAL VRHRVSLFGT DAPAVVNCL HILARSLDAR TVMKSGPEIV KAGLRSFFES ASEDIEKMVE NLRLGKVSQA R TQVKGVGQ NLTYTTVALL PVLTTLFQHI AQHQFGDDVI LDDVQVSCYR TLCSIYSLGT TR NPYVEKL RPALGECLAR LAAAMPVAFL EPQLNEYNAC SVYTTKSPRE RAILGLPNSV EEM CPDIPV LERLMADIGG LAESGARYTE MPHVIEITLP MLCSYLPRWW ERGPEAPPPA LPAG APPPC TAVTSDHLNS LLGNILRIIV NNLGIDEASW MKRLAVFAQP IVSRARPELL HSHFI PTIG RLRKRAGKVV AEEEQLRLEA KAEAEEGELL VRDEFSVLCR DLYALYPLLI RYVDNN RAH WLTEPNPSAE ELFRMVGEIF IYWSKSHNFK REEQNFVVQN EINNMSFLTA DNKSKMA KS GGSDQERTKK KRLGDRYSVQ TSLIVATLKK MLPIGLNMCA PTDQELITLA KTRYALKD T DEEVREFLQN NLHLQGKVEG SPSLRWQMAL YRGLPGREED ADDPEKIVRR VQEVSAVLY HLEQMEHPYK SKKAVWHKLL SKQRRRAVVA CFRMTPLYNL PTHRACNMFL ESYKAAWILT EDHSFEDRM IDDLSKAGEQ EEEEEEVEEK KPDPLHQLVL HFSRTALTEK SKLDEDYLYM A YADIMAKS CHLEEGGENG EAQEEVEVSF EEKEMEKQRL LYQQARLHNR GAAEMVLQMI SA CKGETGA MVSSTLKLGI SILNGGNADV QQKMLDYLKD KKEVGFFQSI QALMQTCSVL DLN AFERQN KAEGLGMVNE DGTVINRQNG EKVMADDEFT QDLFRFLQLL CEGHNNDFQN YLRT QTGNT TTINIIICTV DYLLRLQESI SDFYWYYSGK DVIEEQGKRN FSKAMSVAKQ VFNSL TEYI QGPCTGNQQS LAHSRLWDAV VGFLHVFAHM MMKLAQDSSQ IELLKELLDL QKDMVV MLL SLLEGNVVNG MIARQMVDML VESSSNVEMI LKFFDMFLKL KDIVGSEAFQ DYVTDPR GL ISKKDFQKAM DSQKQFTGPE IQFLLSCSEA DENEMIDCEE FANRFQEPAR DIGFNVAV L LTNLSEHVPH DPRLRNFLEL AESILEYFRP YLGRIEIMGA SRRIERIYFE ISETNRAQW EMPQVKESKR QFIFDVVNEG GESEKMELFV SFCEDTIFEM QIAAQISEPE GEPEEDEDEG AGLAEAGAE GAEEGAVGPE GAAGTAAAGL TARLAAATSR ALRGLSYRSL RRRVRRLRRL T AREAATAL AALLWAALAH AGAAGAGAAA GALRLLWGSL FGGGLVEGAK KVTVTELLAG MP DPTGDEV HGEQPAGPGG EADGEGAGEG AGEAWEGAGD EEVAVQEAGP GGADGAVAVA EGG PFRPEG AGGLGDMGDT TPAEPPTPEG SPIIKRKLGV DGEEEELPPE PEPEPEPEPE KADA ENGEK EEVPKPPPEP PKKTAPPPPP PKKEEGGSGG LEFWGELEVQ RVKFLNYLSR NFYTL RFLA LFLAFAINFI LLFYKVSDSP PGEDDMEGSA AGDLSGAGSG GGSGWGSGAG EEVEGD EDE NMVYYFLEES TGYMEPALRC LSLLHTLVAF LCIIGYNCLK VPLVIFKREK ELARKLE FD GLYITEQPED DDVKGQWDRL VLNTPSFPSN YWDKFVKRKV LDKHGDIYGR ERIAELLG M DLATLEITAH NERKPEPPPG LLTWLMSIDV KYQIWKFGVI FTDNSFLYLG WYMVMSLLG HYNNFFFAAH LLDIAMGVKT LRTILSSVTH NGKQLVMTVG LLAVVVYLYT VVAFNFFRKF YNKSEDEDE PDMKCDDMMT CYLFHMYVGV RAGGGIGDEI EDPAGDEYEL YRVVFDITFF F FVIVILLA IIQGLIIDAF GELRDQQEQV REDMETKCFI CGIGSDYFDT TPHRFETHTL EE HNLANYM FFLMYLINKD ETEHTGQESY VWKMYQERCW DFFPAGDCFR KQYEDQLS UniProtKB: Ryanodine receptor 1 |
-Macromolecule #2: Peptidyl-prolyl cis-trans isomerase FKBP1B
| Macromolecule | Name: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Recombinant expression | Organism: ![]() |
| Sequence | String: GVEIETISPG DGRTFPKKGQ TCVVHYTGML QNGKKFDSSR DRNKPFKFRI GKQEVIKGF EEGAAQMSLG QRAKLTCTPD VAYGATGHPG VIPPNATLIF DVELLNLE UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B |
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 9 mg/mL | ||||||||||||||||||||||||
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| Buffer | pH: 7.5 Component:
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| Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 25 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 3.9e-05 kPa | ||||||||||||||||||||||||
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Specialist optics | Energy filter - Name: TFS Selectris |
| Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 5007 / Average electron dose: 50.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
Canada, 1 items
Citation
























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Y (Row.)
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Processing
FIELD EMISSION GUN

