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基本情報
登録情報 | ![]() | ||||||||||||
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タイトル | Engineered human dynein motor domain in the microtubule-unbound state with LIS1 complex in the buffer containing ATP-Vi (local refined on AAA3-AAA5 and LIS1) | ||||||||||||
![]() | Unsharpened map of engineered human dynein motor domain in microtubule-unbound state with LIS1 complex in buffer containing ATP-Vi (local refined on AAA3-AAA5 and LIS1 region) | ||||||||||||
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![]() | Dynein / motor domain / microtubule-unbound / MOTOR PROTEIN / LIS1 | ||||||||||||
機能・相同性 | ![]() corpus callosum morphogenesis / establishment of planar polarity of embryonic epithelium / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / interneuron migration / 1-alkyl-2-acetylglycerophosphocholine esterase complex / maintenance of centrosome location / microtubule sliding / selenocysteine biosynthetic process / microtubule organizing center organization ...corpus callosum morphogenesis / establishment of planar polarity of embryonic epithelium / microtubule cytoskeleton organization involved in establishment of planar polarity / ameboidal-type cell migration / interneuron migration / 1-alkyl-2-acetylglycerophosphocholine esterase complex / maintenance of centrosome location / microtubule sliding / selenocysteine biosynthetic process / microtubule organizing center organization / platelet activating factor metabolic process / acrosome assembly / radial glia-guided pyramidal neuron migration / cerebral cortex neuron differentiation / seryl-tRNA aminoacylation / serine-tRNA ligase / serine-tRNA ligase activity / positive regulation of intracellular transport / central region of growth cone / positive regulation of embryonic development / regulation of metaphase plate congression / establishment of centrosome localization / reelin-mediated signaling pathway / positive regulation of cytokine-mediated signaling pathway / cortical microtubule organization / establishment of spindle localization / astral microtubule / positive regulation of spindle assembly / nuclear membrane disassembly / layer formation in cerebral cortex / auditory receptor cell development / vesicle transport along microtubule / stem cell division / positive regulation of dendritic spine morphogenesis / stereocilium / myeloid leukocyte migration / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / minus-end-directed microtubule motor activity / microtubule plus-end binding / negative regulation of JNK cascade / osteoclast development / retrograde axonal transport / dynein light intermediate chain binding / cytoplasmic dynein complex / P-body assembly / brain morphogenesis / motile cilium / nuclear migration / microtubule associated complex / kinesin complex / dynein intermediate chain binding / cochlea development / dynein complex binding / cytoplasmic microtubule / transmission of nerve impulse / cell leading edge / establishment of mitotic spindle orientation / germ cell development / dynactin binding / phospholipase binding / microtubule-based process / neuromuscular process controlling balance / protein secretion / neuroblast proliferation / positive regulation of axon extension / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / regulation of microtubule cytoskeleton organization / lipid catabolic process / cytoplasmic microtubule organization / stress granule assembly / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / JNK cascade / regulation of mitotic spindle organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / axon cytoplasm / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / AURKA Activation by TPX2 / positive regulation of mitotic cell cycle / mitotic spindle organization / adult locomotory behavior / filopodium / hippocampus development / RHO GTPases Activate Formins / phosphoprotein binding / HCMV Early Events / neuron migration / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / kinetochore / cerebral cortex development / microtubule cytoskeleton organization 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.3 Å | ||||||||||||
![]() | Ton W / Wang Y / Chai P | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Microtubule-binding-induced allostery triggers LIS1 dissociation from dynein prior to cargo transport. 著者: William D Ton / Yue Wang / Pengxin Chai / Cisloynny Beauchamp-Perez / Nicholas T Flint / Lindsay G Lammers / Hao Xiong / Kai Zhang / Steven M Markus / ![]() 要旨: The lissencephaly-related protein LIS1 is a critical regulator of cytoplasmic dynein that governs motor function and intracellular localization (for example, to microtubule plus-ends). Although LIS1 ...The lissencephaly-related protein LIS1 is a critical regulator of cytoplasmic dynein that governs motor function and intracellular localization (for example, to microtubule plus-ends). Although LIS1 binding is required for dynein activity, its unbinding prior to initiation of cargo transport is equally important, since preventing dissociation leads to dynein dysfunction. To understand whether and how dynein-LIS1 binding is modulated, we engineered dynein mutants locked in a microtubule-bound (MT-B) or microtubule-unbound (MT-U) state. Whereas the MT-B mutant exhibits low LIS1 affinity, the MT-U mutant binds LIS1 with high affinity, and as a consequence remains almost irreversibly associated with microtubule plus-ends. We find that a monomeric motor domain is sufficient to exhibit these opposing LIS1 affinities, and that this is evolutionarily conserved between yeast and humans. Three cryo-EM structures of human dynein with and without LIS1 reveal microtubule-binding induced conformational changes responsible for this regulation. Our work reveals key biochemical and structural insight into LIS1-mediated dynein activation. | ||||||||||||
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マップデータ | ![]() | 89.9 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 23.7 KB 23.7 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 11.8 KB | 表示 | ![]() |
画像 | ![]() | 73.4 KB | ||
マスクデータ | ![]() | 178 MB | ![]() | |
Filedesc metadata | ![]() | 8.8 KB | ||
その他 | ![]() ![]() | 165 MB 165 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 1.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.2 MB | 表示 | |
XML形式データ | ![]() | 20.9 KB | 表示 | |
CIF形式データ | ![]() | 27.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||
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注釈 | Unsharpened map of engineered human dynein motor domain in microtubule-unbound state with LIS1 complex in buffer containing ATP-Vi (local refined on AAA3-AAA5 and LIS1 region) | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.149 Å | ||||||||||||||||||||
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | ![]() | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map A of engineered human dynein motor...
ファイル | emd_29014_half_map_1.map | ||||||||||||
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注釈 | Half map A of engineered human dynein motor domain in microtubule-unbound state with LIS1 complex in buffer containing ATP-Vi (local refined on AAA3-AAA5 and LIS1 region) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map B of engineered human dynein motor...
ファイル | emd_29014_half_map_2.map | ||||||||||||
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注釈 | Half map B of engineered human dynein motor domain in microtubule-unbound state with LIS1 complex in buffer containing ATP-Vi (local refined on AAA3-AAA5 and LIS1 region) | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
-全体 : Engineered human dynein motor domain in microtubule-unbound state...
全体 | 名称: Engineered human dynein motor domain in microtubule-unbound state with LIS1 complex in the buffer containing ATP-Vi |
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要素 |
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-超分子 #1: Engineered human dynein motor domain in microtubule-unbound state...
超分子 | 名称: Engineered human dynein motor domain in microtubule-unbound state with LIS1 complex in the buffer containing ATP-Vi タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#2 |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 490 KDa |
-分子 #1: Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase
分子 | 名称: Cytoplasmic dynein 1 heavy chain 1,Serine--tRNA ligase タイプ: protein_or_peptide / ID: 1 詳細: residues 1458-3277 of dynein followed by residues 30-96 of serine-tRNA ligase, followed by residues 3412-4646 of dynein コピー数: 1 / 光学異性体: LEVO / EC番号: serine-tRNA ligase |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 357.459125 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: GSALEEFLKQ IREVWNTYEL DLVNYQNKCR LIRGWDDLFN KVKEHINSVS AMKLSPYYKV FEEDALSWED KLNRIMALFD VWIDVQRRW VYLEGIFTGS ADIKHLLPVE TQRFQSISTE FLALMKKVSK SPLVMDVLNI QGVQRSLERL ADLLGKIQKA L GEYLERER ...文字列: GSALEEFLKQ IREVWNTYEL DLVNYQNKCR LIRGWDDLFN KVKEHINSVS AMKLSPYYKV FEEDALSWED KLNRIMALFD VWIDVQRRW VYLEGIFTGS ADIKHLLPVE TQRFQSISTE FLALMKKVSK SPLVMDVLNI QGVQRSLERL ADLLGKIQKA L GEYLERER SSFPRFYFVG DEDLLEIIGN SKNVAKLQKH FKKMFAGVSS IILNEDNSVV LGISSREGEE VMFKTPVSIT EH PKINEWL TLVEKEMRVT LAKLLAESVT EVEIFGKATS IDPNTYITWI DKYQAQLVVL SAQIAWSENV ETALSSMGGG GDA APLHSV LSNVEVTLNV LADSVLMEQP PLRRRKLEHL ITELVHQRDV TRSLIKSKID NAKSFEWLSQ MRFYFDPKQT DVLQ QLSIQ MANAKFNYGF EYLGVQDKLV QTPLTDRCYL TMTQALEARL GGSPFGPAGT GKTESVKALG HQLGRFVLVF NCDET FDFQ AMGRIFVGLC QVGAWGCFDE FNRLEERMLS AVSQQVQCIQ EALREHSNPN YDKTSAPITC ELLNKQVKVS PDMAIF ITM NPGYAGRSNL PDNLKKLFRS LAMTKPDRQL IAQVMLYSQG FRTAEVLANK IVPFFKLCDE QLSSQSHYDF GLRALKS VL VSAGNVKRER IQKIKREKEE RGEAVDEGEI AENLPEQEIL IQSVCETMVP KLVAEDIPLL FSLLSDVFPG VQYHRGEM T ALREELKKVC QEMYLTYGDG EEVGGMWVEK VLQLYQITQI NHGLMMVGPS GSGKSMAWRV LLKALERLEG VEGVAHIID PKAISKDHLY GTLDPNTREW TDGLFTHVLR KIIDSVRGEL QKRQWIVFDG DVDPEWVENL NSVLDDNKLL TLPNGERLSL PPNVRIMFE VQDLKYATLA TVSRCGMVWF SEDVLSTDMI FNNFLARLRS IPLDEGEDEA QRRRKGKEDE GEEAASPMLQ I QRDAATIM QPYFTSNGLV TKALEHAFQL EHIMDLTRLR CLGSLFSMLH QACRNVAQYN ANHPDFPMQI EQLERYIQRY LV YAILWSL SGDSRLKMRA ELGEYIRRIT TVPLPTAPNI PIIDYEVSIS GEWSPWQAKV PQIEVETHKV AAPDVVVPTL DTV RHEALL YTWLAEHKPL VLCGPPGSGK TMTLFSALRA LPDMEVVGLN FSSATTPELL LKTFDHYCEY RRTPNGVVLA PVQL GKWLV LFCDEINLPD MDKYGTQRVI SFIRQMVEHG GFYRTSDQTW VKLERIQFVG ACNPPTDPGR KPLSHRFLRH VPVVY VDYP GPASLTQIYG TFNRAMLRLI PSLRTYAEPL TAAMVEFYTM SQERFTQDTQ PHYIYSPREM TRWVRGIFEA LRPLET LPV EGLIRIWAHE ALRLFQDRLV EDEERRWTDE NIDTVALKHF PNIDREKAMS RPILYSNWLS KDYIPVDQEE LRDYVKA RL KVFYEEELDV PLVLFNEVLD HVLRIDRIFR QPQGHLLLIG VSGAGKTTLS RFVAWMNGLS VYQIKVHRKY TGEDFDED L RTVLRRSGCK NEKIAFIMDE SNVLDSGFLE RMNTLLANGE VPGLFEGDEY ATLMTQCKEG AQKEGLMLDS HEELYKWFT SQVIRNLHVV FTMNPSSEGL KDRAATSPAL FNRCVLNWFG DWSTEALYQV GKEFTSKMDL EKPNYIVPDY MPVVYDKLPQ PPSHREAIV NSCVFVHQTL HQANARLAKR GGRTMAITPR HYLDFINHYA NLFHEKRSEL EEQQMHLNVG LRKIKETVDQ V EELRRDLR IKSQELEVKN AAANDKLKKM VKDQQEAEKK KVMSQEIQEQ LHKQQEVIAD KQMSLLALDQ EVQELKKRLQ EV QTERNQV AKRVPKAPPE EKEALIARGR ALGEEAKRLE EALREKEAQL EALRNELQKL EDDAKDNQQK ANEVEQMIRD LEA SIARYK EEYAVLISEA QAIKADLAAV EAKVNRSTAL LKSLSAERER WEKTSETFKN QMSTIAGDCL LSAAFIAYAG YFDQ QMRQN LFTTWSHHLQ QANIQFRTDI ARTEYLSNAD ERLRWQASSL PADDLCTENA IMLKRFNRYP LIIDPSGQAT EFIMN EYKD RKITRTSFLD DAFRKNLESA LRFGNPLLVQ DVESYDPVLN PVLNREVRRT GGRVLITLGD QDIDLSPSFV IFLSTR DPT VEFPPDLCSR VTFVNFTVTR SSLQSQCLNE VLKAERPDVD EKRSDLLKLQ GEFQLRLRQL EKSLLQALNE VKGRILD DD TIITTLENLK REAAEVTRKV EETDIVMQEV ETVSQQYLPL STACSSIYFT MESLKQIHFL YQYSLQFFLD IYHNVLYE N PNLKGVTDHT QRLSIITKDL FQVAFNRVAR GMLHQDHITF AMLLARIKLK GTVGEPTYDA EFQHFLRGNE IVLSAGSTP RIQGLTVEQA EAVVRLSCLP AFKDLIAKVQ ADEQFGIWLD SSSPEQTVPY LWSEETPATP IGQAIHRLLL IQAFRPDRLL AMAHMFVST NLGESFMSIM EQPLDLTHIV GTEVKPNTPV LMCSVPGYDA SGHVEDLAAE QNTQITSIAI GSAEGFNQAD K AINTAVKS GRWVMLKNVH LAPGWLMQLE KKLHSLQPHA CFRLFLTMEI NPKVPVNLLR AGRIFVFEPP PGVKANMLRT FS SIPVSRI CKSPNERARL YFLLAWFHAI IQERLRYAPL GWSKKYEFGE SDLRSACDTV DTWLDDTAKG RQNISPDKIP WSA LKTLMA QSIYGGRVDN EFDQRLLNTF LERLFTTRSF DSEFKLACKV DGHKDIQMPD GIRREEFVQW VELLPDTQTP SWLG LPNNA ERVLLTTQGV DMISKMLKMQ MLEDEDDLAY AETEKKTRTD STSDGRPAWM RTLHTTASNW LHLIPQTLSH LKRTV ENIK DPLFRFFERE VKMGAKLLQD VRQDLADVVQ VCEGKKKQTN YLRTLINELV KGILPRSWSH YTVPAGMTVI QWVSDF SER IKQLQNISLA AASGGAKELK NIHVCLGGLF VPEAYITATR QYVAQANSWS LEELCLEVNV TTSQGATLDA CSFGVTG LK LQGATCNNNK LSLSNAISTA LPLTQLRWVK QTNTEKKASV VTLPVYLNFT RADLIFTVDF EIATKEDPRS FYERGVAV L CTEEF UniProtKB: Cytoplasmic dynein 1 heavy chain 1, Serine--tRNA ligase, Cytoplasmic dynein 1 heavy chain 1 |
-分子 #2: Platelet-activating factor acetylhydrolase IB subunit beta,Platel...
分子 | 名称: Platelet-activating factor acetylhydrolase IB subunit beta,Platelet-activating factor acetylhydrolase IB subunit beta,human LIS1 protein with a SNAP tag タイプ: protein_or_peptide / ID: 2 詳細: SNAP tag present on C-terminus,SNAP tag present on C-terminus コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 66.423547 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: GSVLSQRQRD ELNRAIADYL RSNGYEEAYS VFKKEAELDV NEELDKKYAG LLEKKWTSVI RLQKKVMELE SKLNEAKEEF TSGGPLGQK RDPKEWIPRP PEKYALSGHR SPVTRVIFHP VFSVMVSASE DATIKVWDYE TGDFERTLKG HTDSVQDISF D HSGKLLAS ...文字列: GSVLSQRQRD ELNRAIADYL RSNGYEEAYS VFKKEAELDV NEELDKKYAG LLEKKWTSVI RLQKKVMELE SKLNEAKEEF TSGGPLGQK RDPKEWIPRP PEKYALSGHR SPVTRVIFHP VFSVMVSASE DATIKVWDYE TGDFERTLKG HTDSVQDISF D HSGKLLAS CSADMTIKLW DFQGFECIRT MHGHDHNVSS VAIMPNGDHI VSASRDKTIK MWEVQTGYCV KTFTGHREWV RM VRPNQDG TLIASCSNDQ TVRVWVVATK ECKAELREHE HVVECISWAP ESSYSSISEA TGSETKKSGK PGPFLLSGSR DKT IKMWDV STGMCLMTLV GHDNWVRGVL FHSGGKFILS CADDKTLRVW DYKNKRCMKT LNAHEHFVTS LDFHKTAPYV VTGS VDQTV KVWECRGAGA GADKDCEMKR TTLDSPLGKL ELSGCEQGLH RIIFLGKGTS AADAVEVPAP AAVLGGPEPL MQATA WLNA YFHQPEAIEE FPVPALHHPV FQQESFTRQV LWKLLKVVKF GEVISYSHLA ALAGNPAATA AVKTALSGNP VPILIP CHR VVQGDLDVGG YEGGLAVKEW LLAHEGHRLG KPGLG UniProtKB: Platelet-activating factor acetylhydrolase IB subunit beta |
-分子 #3: ADENOSINE-5'-DIPHOSPHATE
分子 | 名称: ADENOSINE-5'-DIPHOSPHATE / タイプ: ligand / ID: 3 / コピー数: 2 / 式: ADP |
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分子量 | 理論値: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.5 mg/mL |
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緩衝液 | pH: 7.4 詳細: 50 mM Tris pH 7.4, 150 mM potassium acetate, 2 mM magnesium acetate, 1 mM EGTA, 1 mM DTT, and 0.1 mM Mg-ATP |
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: GRAPHENE OXIDE / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 1 / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 60 sec. / 前処理 - 雰囲気: AIR |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 検出モード: SUPER-RESOLUTION / 平均電子線量: 40.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 100.0 µm / 最大 デフォーカス(補正後): 3.0 µm / 最小 デフォーカス(補正後): 1.2 µm / 倍率(補正後): 105000 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 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): 1.2 µm / 倍率(公称値): 105000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT |
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得られたモデル | ![]() PDB-8fdu: |