+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4295 | |||||||||
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タイトル | Structure of Ryanodine Receptor 1 in nanodiscs in the presence of calcium and ATP | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | calcium release channel / nanodiscs / MEMBRANE PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 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 / skin development / organelle membrane / cellular response to caffeine / outflow tract morphogenesis ...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 / skin development / organelle membrane / cellular response to caffeine / outflow tract morphogenesis / intracellularly gated calcium channel activity / toxic substance binding / voltage-gated calcium channel activity / smooth endoplasmic reticulum / skeletal muscle fiber development / striated muscle contraction / muscle contraction / release of sequestered calcium ion into cytosol / sarcoplasmic reticulum membrane / cellular response to calcium ion / sarcoplasmic reticulum / calcium ion transmembrane transport / calcium channel activity / sarcolemma / Z disc / intracellular calcium ion homeostasis / disordered domain specific binding / protein homotetramerization / transmembrane transporter binding / calmodulin binding / calcium ion binding / ATP binding / identical protein binding / membrane 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 8.2 Å | |||||||||
データ登録者 | Willegems K / Efremov RG | |||||||||
資金援助 | ベルギー, 2件
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引用 | ジャーナル: Structure / 年: 2018 タイトル: Influence of Lipid Mimetics on Gating of Ryanodine Receptor. 著者: Katrien Willegems / Rouslan G Efremov / 要旨: Understanding gating principles of ion channels at high resolution is of great importance. Here we investigate the conformational transition from closed to open state in ryanodine receptor 1 (RyR1) ...Understanding gating principles of ion channels at high resolution is of great importance. Here we investigate the conformational transition from closed to open state in ryanodine receptor 1 (RyR1) reconstituted into lipid nanodiscs. RyR1 is a homotetrameric giant ion channel that couples excitation of muscle cells to fast calcium release from the sarcoplasmic reticulum. Using single-particle cryo-EM we show that RyR1 reconstituted into lipid nanodiscs is stabilized in the open conformation when bound to the plant toxin ryanodine, but not in the presence of its physiological activators, calcium and ATP. Further, using ryanodine binding assays we show that membrane mimetics influence RyR1 transition between closed and open-channel conformations. We find that all detergents, including fluorinated detergents added to nanodiscs, stabilize closed state of RyR1. Our biochemical results correlate with available structural data and suggest optimal conditions for structural studies of RyR1 gating. | |||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_4295.map.gz | 163.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4295-v30.xml emd-4295.xml | 24.6 KB 24.6 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_4295_fsc.xml | 12.3 KB | 表示 | FSCデータファイル |
画像 | emd_4295.png | 133.4 KB | ||
Filedesc metadata | emd-4295.cif.gz | 8.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4295 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4295 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_4295_validation.pdf.gz | 297.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_4295_full_validation.pdf.gz | 296.8 KB | 表示 | |
XML形式データ | emd_4295_validation.xml.gz | 12.4 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4295 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4295 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_4295.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.645 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
-全体 : Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP
全体 | 名称: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP |
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要素 |
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-超分子 #1: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP
超分子 | 名称: Ryanodine receptor 1 in nanodiscs in presence of calcium and ATP タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1 |
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由来(天然) | 生物種: Oryctolagus cuniculus (ウサギ) / 株: New Zealand white rabbit / 組織: skeletal muscle / 細胞中の位置: sarcoplasmic reticulum |
分子量 | 理論値: 2.2 MDa |
-分子 #1: Ryanodine receptor 1
分子 | 名称: Ryanodine receptor 1 / タイプ: protein_or_peptide / ID: 1 / コピー数: 4 / 光学異性体: LEVO |
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由来(天然) | 生物種: Oryctolagus cuniculus (ウサギ) / 組織: skeletal muscle |
分子量 | 理論値: 532.709688 KDa |
配列 | 文字列: MGDGGEGEDE VQFLRTDDEV VLQCSATVLK EQLKLCLAAE GFGNRLCFLE PTSNAQNVPP DLAICCFTLE QSLSVRALQE MLANTVEAG VESSQGGGHR TLLYGHAILL RHAHSRMYLS CLTTSRSMTD KLAFDVGLQE DATGEACWWT MHPASKQRSE G EKVRVGDD ...文字列: 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 VQF(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)MPLSA AMFLSERKNP APQCPPRLEV QMLMPVSWSR MPNHFLQVET RRAGERLGW AVQCQDPLTM MALHIPEENR CMDILELSER LDLQRFHSHT LRLYRAVCAL GNNRVAHALC SHVDQAQLLH A LEDAHLPG PLRAGYYDLL ISIHLESACR SRRSMLSEYI VPLTPETRAI TLFPPGRKGG NARRHGLPGV GVTTSLRPPH HF SPPCFVA ALPAAGVAEA PARLSPAIPL EALRDKALRM LGEAVRDGGQ HARDPVGGSV EFQFVPVLKL VSTLLVMGIF GDE DVKQIL KMIEPEVFTE EEEEEEEEEE EEEEEEEDEE EKEEDEEEEE KEDAEKEEEE APEGEKEDLE EGLLQMKLPE SVKL QMCNL LEYFCDQELQ HRVESLAAFA ERYVDKLQAN QRSRYALLMR AFTMSAAETA RRTREFRSPP QEQINMLLHF KDEAD EEDC PLPEDIRQDL QDFHQDLLAH CGIQLEGEEE EPEEETSLSS RLRSLLETVR LVKKKEEKPE EELPAEEKKP QSLQEL VSH MVVRWAQEDY VQSPELVRAM FSLLHRQYDG LGELLRALPR AYTISPSSVE DTMSLLECLG QIRSLLIVQM GPQEENL MI QSIGNIMNNK VFYQHPNLMR ALGMHETVME VMVNVLGGGE TKEIRFPKMV TSCCRFLCYF CRISRQNQRS MFDHLSYL L ENSGIGLGMQ GSTPLDVAAA SVIDNNELAL ALQEQDLEKV VSYLAGCGLQ SCPMLLAKGY PDIGWNPCGG ERYLDFLRF AVFVNGESVE ENANVVVRLL IRKPECFGPA LRGEGGSGLL AAIEEAIRIS EDPARDGPGV RRDRRREHFG EEPPEENRVH LGHAIMSFY AALIDLLGRC APEMHLIQAG KGEALRIRAI LRSLVPLDDL VGIISLPLQI PTL(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(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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(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) TPLYN LPTHRACNMF LESYKAAWIL TEDHSFEDRM IDDLSKAGEQ EEEEEEVEEK KPDPLHQLVL HFSRTALTEK SKLDE DYLY MAYADIMAKS CHLEEGGENG EAEEEEVEVS FEEKEMEKQR LLYQQSRLHT RGAAEMVLQM ISACKGETGA MVSSTL KLG ISILNGGNAE VQQKMLDYLK DKKEVGFFQS IQALMQTCSV LDLNAFERQN KAEGLGMVNE DGTVINRQNG EKVMADD EF TQDLFRFLQL LCEGHNNDFQ NYLRTQTGNT TTINIIICTV DYLLRLQESI SDFYWYYSGK DVIEEQGKRN FSKAMSVA K QVFNSLTEYI QGPCTGNQQS LAHSRLWDAV VGFLHVFAHM MMKLAQDSSQ IELLKELLDL QKDMVVMLLS LLEGNVVNG MIARQMVDML VESSSNVEMI LKFFDMFLKL KDIVGSEAFQ DYVTDPRGLI SKKDFQKAMD SQKQFTGPEI QFLLSCSEAD ENEMINFEE FANRFQEPAR DIGFNVAVLL TNLSEHVPHD PRLRNFLELA ESILEYFRPY LGRIEIMGAS RRIERIYFEI S ETNRAQWE MPQVKESKRQ FIFDVVNEGG EAEKMELFVS FCEDTIFEMQ IAAQISEPEG EPEADEDEGM GEAAAEGAEE GA AGAEGAA GTVAAGATAR LAAAAARALR GLSYRSLRRR VRRLRRLTAR EAATALAALL WAVVARAGAA GAGAAAGALR LLW GSLFGG GLVEGAKKVT VTELLAGMPD PTSDEVHGEQ PAGPGGDADG AGEGEGEGDA AEGDGDEEVA GHEAGPGGAE GVVA VADGG PFRPEGAGGL GDMGDTTPAE PPTPEGSPIL KRKLGVDGEE EELVPEPEPE PEPEPEKADE ENGEKEEVPE APPEP PKKA PPSPPAKKEE AGGAGMEFWG ELEVQRVKFL NYLSRNFYTL RFLALFLAFA INFILLFYKV SDSPPGEDDM EGSAAG DLA GAGSGGGSGW GSGAGEEAEG DEDENMVYYF LEESTGYMEP ALWCLSLLHT LVAFLCIIGY NCLKVPLVIF KREKELA RK LEFDGLYITE QPGDDDVKGQ WDRLVLNTPS FPSNYWDKFV KRKVLDKHGD IFGRERIAEL LGMDLASLEI TAHNERKP D PPPGLLTWLM SIDVKYQIWK FGVIFTDNSF LYLGWYMVMS LLGHYNNFFF AAHLLDIAMG VKTLRTILSS VTHNGKQLV MTVGLLAVVV YLYTVVAFNF FRKFYNKSED EDEPDMKCDD MMTCYLFHMY VGVRAGGGIG DEIEDPAGDE YELYRVVFDI TFFFFVIVI LLAIIQGLII DAFGELRDQQ EQVKEDMETK CFICGIGSDY FDTTPHGFET HTLEEHNLAN YMFFLMYLIN K DETEHTGQ ESYVWKMYQE RCWDFFPAGD CFRKQYEDQL S UniProtKB: Ryanodine receptor 1, Ryanodine receptor 1, Ryanodine receptor 1, Ryanodine receptor 1 |
-分子 #2: ZINC ION
分子 | 名称: ZINC ION / タイプ: ligand / ID: 2 / コピー数: 4 / 式: ZN |
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分子量 | 理論値: 65.409 Da |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 3 mg/mL | ||||||||||||||||||||||||
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緩衝液 | pH: 7.4 構成要素:
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グリッド | モデル: Quantifoil R2/1 / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 60 sec. / 前処理 - 雰囲気: AIR / 前処理 - 気圧: 0.0004 kPa | ||||||||||||||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内温度: 293.15 K / 装置: HOMEMADE PLUNGER | ||||||||||||||||||||||||
詳細 | Protein was reconstituted into lipid nanodiscs |
-電子顕微鏡法
顕微鏡 | FEI TALOS ARCTICA |
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撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 検出モード: COUNTING / デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / デジタル化 - 画像ごとのフレーム数: 1-16 / 撮影したグリッド数: 1 / 実像数: 1906 / 平均電子線量: 1.7 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 2.0 µm / 倍率(公称値): 92000 |
試料ステージ | ホルダー冷却材: NITROGEN |
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL |
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得られたモデル | PDB-6foo: |