+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32036 | |||||||||||||||||||||
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Title | Structure of recombinant RyR2 mutant K4593A (EGTA dataset) | |||||||||||||||||||||
Map data | Structure of recombinant RyR2 mutant K4593A (EGTA dataset) | |||||||||||||||||||||
Sample |
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Keywords | CALCIUM / CALCIUM CHANNEL / CALCIUM TRANSPORT / ION TRANSPORT / IONIC CHANNEL / METAL TRANSPORT / ER/SR MEMBRANE / RYANODINE RECEPTOR / RYANODINE / RECEPTOR / WILD TYPE / MEMBRANE PROTEIN | |||||||||||||||||||||
Function / homology | Function and homology information manganese ion transmembrane transport / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / suramin binding / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / organic cyclic compound binding / regulation of AV node cell action potential ...manganese ion transmembrane transport / establishment of protein localization to endoplasmic reticulum / type B pancreatic cell apoptotic process / Purkinje myocyte to ventricular cardiac muscle cell signaling / suramin binding / regulation of SA node cell action potential / regulation of atrial cardiac muscle cell action potential / left ventricular cardiac muscle tissue morphogenesis / organic cyclic compound binding / regulation of AV node cell action potential / calcium-induced calcium release activity / sarcoplasmic reticulum calcium ion transport / Stimuli-sensing channels / Ion homeostasis / regulation of ventricular cardiac muscle cell action potential / ventricular cardiac muscle cell action potential / positive regulation of sequestering of calcium ion / cyclic nucleotide binding / negative regulation of calcium-mediated signaling / embryonic heart tube morphogenesis / cardiac muscle hypertrophy / negative regulation of insulin secretion involved in cellular response to glucose stimulus / calcium ion transport into cytosol / negative regulation of release of sequestered calcium ion into cytosol / neuronal action potential propagation / insulin secretion involved in cellular response to glucose stimulus / ryanodine-sensitive calcium-release channel activity / response to caffeine / response to muscle activity / A band / release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / calcium ion transmembrane import into cytosol / response to redox state / protein maturation by protein folding / 'de novo' protein folding / negative regulation of heart rate / positive regulation of heart rate / FK506 binding / negative regulation of cytosolic calcium ion concentration / positive regulation of axon regeneration / protein kinase A regulatory subunit binding / extrinsic component of cytoplasmic side of plasma membrane / cellular response to caffeine / channel regulator activity / protein kinase A catalytic subunit binding / response to magnesium ion / positive regulation of the force of heart contraction / intracellularly gated calcium channel activity / detection of calcium ion / smooth muscle contraction / response to vitamin E / smooth endoplasmic reticulum / regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion / calcium channel inhibitor activity / striated muscle contraction / regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum / T cell proliferation / Ion homeostasis / release of sequestered calcium ion into cytosol / regulation of cytosolic calcium ion concentration / calcium channel complex / cellular response to epinephrine stimulus / sarcoplasmic reticulum membrane / response to muscle stretch / regulation of heart rate / sarcomere / sarcoplasmic reticulum / establishment of localization in cell / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / calcium-mediated signaling / calcium ion transmembrane transport / response to hydrogen peroxide / calcium channel activity / Stimuli-sensing channels / sarcolemma / Z disc / response to calcium ion / intracellular calcium ion homeostasis / calcium ion transport / nuclear envelope / positive regulation of cytosolic calcium ion concentration / monoatomic ion transmembrane transport / protein refolding / scaffold protein binding / transmembrane transporter binding / response to hypoxia / calmodulin binding / signaling receptor binding / calcium ion binding / protein kinase binding / enzyme binding / protein-containing complex / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Mus musculus (house mouse) / Homo sapiens (human) | |||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||||||||||||||
Authors | Kobayashi T / Tsutsumi A | |||||||||||||||||||||
Funding support | Japan, 6 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Molecular basis for gating of cardiac ryanodine receptor explains the mechanisms for gain- and loss-of function mutations. Authors: Takuya Kobayashi / Akihisa Tsutsumi / Nagomi Kurebayashi / Kei Saito / Masami Kodama / Takashi Sakurai / Masahide Kikkawa / Takashi Murayama / Haruo Ogawa / Abstract: Cardiac ryanodine receptor (RyR2) is a large Ca release channel in the sarcoplasmic reticulum and indispensable for excitation-contraction coupling in the heart. RyR2 is activated by Ca and RyR2 ...Cardiac ryanodine receptor (RyR2) is a large Ca release channel in the sarcoplasmic reticulum and indispensable for excitation-contraction coupling in the heart. RyR2 is activated by Ca and RyR2 mutations are implicated in severe arrhythmogenic diseases. Yet, the structural basis underlying channel opening and how mutations affect the channel remains unknown. Here, we address the gating mechanism of RyR2 by combining high-resolution structures determined by cryo-electron microscopy with quantitative functional analysis of channels carrying various mutations in specific residues. We demonstrated two fundamental mechanisms for channel gating: interactions close to the channel pore stabilize the channel to prevent hyperactivity and a series of interactions in the surrounding regions is necessary for channel opening upon Ca binding. Mutations at the residues involved in the former and the latter mechanisms cause gain-of-function and loss-of-function, respectively. Our results reveal gating mechanisms of the RyR2 channel and alterations by pathogenic mutations at the atomic level. | |||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32036.map.gz | 116.8 MB | EMDB map data format | |
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Header (meta data) | emd-32036-v30.xml emd-32036.xml | 22.7 KB 22.7 KB | Display Display | EMDB header |
Images | emd_32036.png | 127.8 KB | ||
Filedesc metadata | emd-32036.cif.gz | 8.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32036 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32036 | HTTPS FTP |
-Validation report
Summary document | emd_32036_validation.pdf.gz | 692.4 KB | Display | EMDB validaton report |
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Full document | emd_32036_full_validation.pdf.gz | 692 KB | Display | |
Data in XML | emd_32036_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_32036_validation.cif.gz | 7.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32036 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32036 | HTTPS FTP |
-Related structure data
Related structure data | 7vmrMC 7vmlC 7vmmC 7vmnC 7vmoC 7vmpC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_32036.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Structure of recombinant RyR2 mutant K4593A (EGTA dataset) | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.328 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : Recombinant RyR2 mutant K4593A in the presence of EGTA
Entire | Name: Recombinant RyR2 mutant K4593A in the presence of EGTA |
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Components |
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-Supramolecule #1: Recombinant RyR2 mutant K4593A in the presence of EGTA
Supramolecule | Name: Recombinant RyR2 mutant K4593A in the presence of EGTA type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 / Details: in complex with FKBP12.6 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Supramolecule #2: Ryanodine receptor 2
Supramolecule | Name: Ryanodine receptor 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: FKBP1B
Supramolecule | Name: FKBP1B / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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-Macromolecule #1: Ryanodine receptor 2
Macromolecule | Name: Ryanodine receptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 533.595438 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MADAGEGEDE IQFLRTDDEV VLQCTATIHK EQQKLCLAAE GFGNRLCFLE STSNSKNVPP DLSICTFVLE QSLSVRALQE MLANTVEKS EGQVDVEKWK FMMKTAQGGG HRTLLYGHAI LLRHSYSGMY LCCLSTSRSS TDKLAFDVGL QEDTTGEACW W TIHPASKQ ...String: MADAGEGEDE IQFLRTDDEV VLQCTATIHK EQQKLCLAAE GFGNRLCFLE STSNSKNVPP DLSICTFVLE QSLSVRALQE MLANTVEKS EGQVDVEKWK FMMKTAQGGG HRTLLYGHAI LLRHSYSGMY LCCLSTSRSS TDKLAFDVGL QEDTTGEACW W TIHPASKQ RSEGEKVRVG DDLILVSVSS ERYLHLSYGN SSWHVDAAFQ QTLWSVAPIS SGSEAAQGYL IGGDVLRLLH GH MDECLTV PSGEHGEEQR RTVHYEGGAV SVHARSLWRL ETLRVAWSGS HIRWGQPFRL RHVTTGKYLS LMEDKNLLLM DKE KADVKS TAFAFRSSKE KLDVGVRKEV DGMGTSEIKY GDSICYIQHV DTGLWLTYQA VDVKSARMGS IQRKAIMHHE GHMD DGLNL SRSQHEESRT ARVIRSTVFL FNRFIRGLDA LSKKVKLPTI DLPIESVSLS LQDLIGYFHP PDEHLEHEDK QNRLR ALKN RQNLFQEEGM INLVLECIDR LHVYSSAAHF ADVAGREAGE SWKSILNSLY ELLAALIRGN RKNCAQFSGS LDWLIS RLE RLEASSGILE VLHCVLVESP EALNIIKEGH IKSIISLLDK HGRNHKVLDV LCSLCVCHGV AVRSNQHLIC DNLLPGR DL LLQTRLVNHV SSMRPNIFLG VSEGSAQYKK WYYELMVDHT EPFVTAEATH LRVGWASTEG YSPYPGGGEE WGGNGVGD D LFSYGFDGLH LWSGCIARTV SSPNQHLLRT DDVISCCLDL SAPSISFRIN GQPVQGMFEN FNIDGLFFPV VSFSAGIKV RFLLGGRHGE FKFLPPPGYA ACYEAVLPKE KLKVEHSREY KQERTYTRDL LGPTVSLTQA AFTPVPVDTS QIVLPPHLER IRERLAENI HELWVMNKIE LGWQYGPVRD DNKRQHPCLV EFCKLPEQER NYNLQMSLET LKTLLALGCH VGIADEHAEE K VKKMKLPK NYQLTSGYKP APMDLSFIKL TPSQEAMVDK LAENAHNVWA RDRIRQGWTY GIQQDVKNRR NPRLVPYTLL DD RTKKSNK DSLREAVRTL LGYGYHLEAP DQDHASRAEV CSGTGERFRI FRAEKTYAVK AGRWYFEFEA VTAGDMRVGW SRP GCQPDL ELGSDDRAFA FDGFKAQRWH QGNEHYGRSW QAGDVVGCMV DMNEHTMMFT LNGEILLDDS GSELAFKDFD VGDG FIPVC SLGVAQVGRM NFGKDVSTLK YFTICGLQEG YEPFAVNTNR DITMWLSKRL PQFLQVPSNH EHIEVTRIDG TIDSS PCLK VTQKSFGSQN NNTDIMFYRL SMPIECA(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)DSD FEVLMKTAHG HLVPDRIDKD KETPKPEFNN HKDYAQEKPS RLKQ(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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LFPDENKKHG LPGIGLSTSL RPRMRFSSPS FVSISNDCYQ YSPEFPLDIL KAKTIQMLTE AVKEGSL HA RDPVGGTTEF LFVPLIKLFY TLLIMGIFHN EDLKHILQLI EPSVFKEAAV PEEEGGTPEK EISIEDAKLE GEEEAKGG K RPKEGLLQMK LPEPVKLQMC LLLQYLCDCQ VRHRIEAIVA FSDDFVAKLQ DNQRFRYNEV MQALNMSAAL TARKTREFR SPPQEQINML LNFKDDKSEC PCPEEIRDQL LDFHEDLMTH CGIELDEDGS LDGSNDLTIR GRLLSLVEKV TYLKKKQAEK PVASDSRKC SSLQQLISET MVRWAQESVI EDPELVRAMF VLLHRQYDGI GGLVRALPKT YTINGVSVED TINLLASLGQ I RSLLSVRM GKEEEKLMIR GLGDIMNNKV FYQHPNLMRA LGMHETVMEV MVNVLGGGES KEITFPKMVA NCCRFLCYFC RI SRQNQKA MFDHLSYLLE NSSVGLASPA MRGSTPLDVA AASVMDNNEL ALALREPDLE KVVRYLAGCG LQSCQMLVSK GYP DIGWNP VEGERYLDFL RFAVFCNGES VEENANVVVR LLIRRPECFG PALRGEGGNG LLAAMEEAIK IAEDPSRDGP SPTS GSSKT LDIEEEEDDT IHMGNAIMTF YAALIDLLGR CAPEMHLIHA GKGEAIRIRS ILRSLIPLGD LVGVISIAFQ MPTIA KDGK VVEPDMSAGF CPDHKAAMVL FLDRVYGIEV QDFLLHLLEV GFLPDLRAAA SLDTAALS(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) 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MKPYKLLSEK EKEIYRWPIK ESLKTMLAWG WRIERTREGD SMALYNRTRR ISQTSQVSID AAHGYSPRAI D MSNVTLSR DLHAMAEMMA ENYHNIWAKK KKLELESKGG GNHPLLVPYD TLTAKEKAKD REKAQDIFKF LQISGYVVSR GF KDLDLDT PS(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(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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ERQNKAEGLG MVTEEGSGEK VLQDDEFTCD LFRFLQLLCE GHNSDFQNYL RTQTGNNTTV NIIISTVDYL LRVQESIS D FYWYYSGKDI IDEQGQRNFS KAIQVAKQVF NTLTEYIQGP CTGNQQSLAH SRLWDAVVGF LHVFAHMQMK LSQDSSQIE LLKELMDLQK DMVVMLLSML EGNVVNGTIG KQMVDMLVES SNNVEMILKF FDMFLKLKDL TSSDTFKEYD PDGKGVISKR DFHKAMESH KHYTQSETEF LLSCAETDEN ETLDYEEFVK RFHEPAKDIG FNVAVLLTNL SEHMPNDTRL QTFLELAESV L NYFQPFLG RIEIMGSAKR IERVYFEISE SSRTQWEKPQ VKESKRQFIF DVVNEGGEKE KMELFVNFCE DTIFEMQLAA QI SESDLNE RLANKEESEK ERPEEQAPRM GFFSLLTIQS ALFALRYNVL TLVRMLSLKS LKKQMKRMKK MTVKDMVLAF FSS YWSVFV TLLHFVASVC RGFFRIVSSL LLGGSLVEGA KKIKVAELLA NMPDPTQDEV RGDEEEGERK PLESALPSED LTDL KELTE ESDLLSDIFG LDLKREGGQY KLIPHNPNAG LSDLMTNPVP VPEVQEKFQE QKAKEEKEEK EETKSEPEKA EGEDG EKEE KAKDEKSKQK LRQLHTHRYG EPEVPESAFW KKIIAYQQKL LNYFARNFYN MRMLALFVAF AINFILLFYK VSTSSV VEG KELPTRTSSD TAKVTNSLDS SPHRIIAVHY VLEESSGYME PTLRILAILH TIISFFCIIG YYCLAVPLVI FKREKEV AR KLEFDGLYIT EQPSEDDIKG QWDRLVINTQ SFPNNYWDKF VKRKVMDKYG EFYGRDRISE LLGMDKAALD FSDAREKK K PKKDSSLSAV LNSIDVKYQM WKLGVVFTDN SFLYLAWYMT MSVLGHYNNF FFAAHLLDIA MGFKTLRTIL SSVTHNGKQ LVLTVGLLAV VVYLYTVVAF NFFRKFYNKS EDGDTPDMKC DDMLTCYMFH MYVGVRAGGG IGDEIEDPAG DEYEIYRIIF DITFFFFVI VILLAIIQGL IIDAFGELRD QQEQVKEDME TKCFICGIGN DYFDTVPHGF ETHTLQEHNL ANYLFFLMYL I NKDETEHT GQESYVWKMY QERCWEFFPA GDCFRKQYED QLN UniProtKB: Ryanodine receptor 2, Ryanodine receptor 2, Ryanodine receptor 2, Ryanodine receptor 2, Ryanodine receptor 2 |
-Macromolecule #2: Peptidyl-prolyl cis-trans isomerase FKBP1B
Macromolecule | Name: Peptidyl-prolyl cis-trans isomerase FKBP1B / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: peptidylprolyl isomerase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 18.984316 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGSSHHHHHH SSGLVPRGSH MASMDEKTTG WRGGHVVEGL AGELEQLRAR LEHHPQGQRE PGSGGSGGTG VEIETISPGD GRTFPKKGQ TCVVHYTGML QNGKKFDSSR DRNKPFKFRI GKQEVIKGFE EGAAQMSLGQ RAKLTCTPDV AYGATGHPGV I PPNATLIF DVELLNLE UniProtKB: Peptidyl-prolyl cis-trans isomerase FKBP1B |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Sugar embedding | Material: buffer |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 68394 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |