+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-8165 | |||||||||
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タイトル | Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution | |||||||||
マップデータ | None | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 RHOBTB2 GTPase cycle / RHOU GTPase cycle / RHOV GTPase cycle / contractile vacuole / COPI-mediated anterograde transport / Platelet degranulation / basal body patch / sorocarp development / myosin II filament / macropinocytic cup ...RHOBTB2 GTPase cycle / RHOU GTPase cycle / RHOV GTPase cycle / contractile vacuole / COPI-mediated anterograde transport / Platelet degranulation / basal body patch / sorocarp development / myosin II filament / macropinocytic cup / tight junction assembly / Neutrophil degranulation / regulation of transepithelial transport / morphogenesis of a polarized epithelium / actin crosslink formation / profilin binding / actin filament-based movement / protein localization to bicellular tight junction / structural constituent of postsynaptic actin cytoskeleton / vocalization behavior / Formation of annular gap junctions / dense body / actomyosin / Gap junction degradation / Cell-extracellular matrix interactions / myosin filament / actomyosin structure organization / RHO GTPases Activate ROCKs / hyperosmotic response / regulation of stress fiber assembly / RHO GTPases activate CIT / Sema4D induced cell migration and growth-cone collapse / Adherens junctions interactions / myosin II complex / Interaction between L1 and Ankyrins / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / regulation of synaptic vesicle endocytosis / apical junction complex / regulation of focal adhesion assembly / sarcomere organization / EPHA-mediated growth cone collapse / microfilament motor activity / positive regulation of wound healing / cortical actin cytoskeleton / myofibril / maintenance of blood-brain barrier / NuA4 histone acetyltransferase complex / cell leading edge / pseudopodium / RHO GTPases activate PAKs / filamentous actin / Recycling pathway of L1 / brush border / actin filament bundle assembly / skeletal muscle contraction / calyx of Held / neuronal action potential / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / RHOBTB2 GTPase cycle / phagocytic vesicle / phagocytosis / stress fiber / skeletal muscle tissue development / RHO GTPases activate PKNs / EPHB-mediated forward signaling / cellular response to starvation / axonogenesis / extracellular matrix / platelet aggregation / cell projection / mitochondrion organization / cell motility / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / RHO GTPases Activate Formins / FCGR3A-mediated phagocytosis / sensory perception of sound / 加水分解酵素; 酸無水物に作用; 酸無水物に作用・細胞または細胞小器官の運動に関与 / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / Schaffer collateral - CA1 synapse / cellular response to type II interferon / structural constituent of cytoskeleton / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / cell-cell junction / actin filament binding / cell junction / Clathrin-mediated endocytosis / regulation of cell shape / cell cortex / protein-macromolecule adaptor activity 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Dictyostelium discoideum (キイロタマホコリカビ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.9 Å | |||||||||
データ登録者 | von der Ecken J / Heissler SM / Pathan-Chhatbar S / Manstein DJ / Raunser S | |||||||||
引用 | ジャーナル: Nature / 年: 2016 タイトル: Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution. 要旨: The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments of the cytoskeleton. The energy for these movements is generated ...The interaction of myosin with actin filaments is the central feature of muscle contraction and cargo movement along actin filaments of the cytoskeleton. The energy for these movements is generated during a complex mechanochemical reaction cycle. Crystal structures of myosin in different states have provided important structural insights into the myosin motor cycle when myosin is detached from F-actin. The difficulty of obtaining diffracting crystals, however, has prevented structure determination by crystallography of actomyosin complexes. Thus, although structural models exist of F-actin in complex with various myosins, a high-resolution structure of the F-actin–myosin complex is missing. Here, using electron cryomicroscopy, we present the structure of a human rigor actomyosin complex at an average resolution of 3.9 Å. The structure reveals details of the actomyosin interface, which is mainly stabilized by hydrophobic interactions. The negatively charged amino (N) terminus of actin interacts with a conserved basic motif in loop 2 of myosin, promoting cleft closure in myosin. Surprisingly, the overall structure of myosin is similar to rigor-like myosin structures in the absence of F-actin, indicating that F-actin binding induces only minimal conformational changes in myosin. A comparison with pre-powerstroke and intermediate (Pi-release) states of myosin allows us to discuss the general mechanism of myosin binding to F-actin. Our results serve as a strong foundation for the molecular understanding of cytoskeletal diseases, such as autosomal dominant hearing loss and diseases affecting skeletal and cardiac muscles, in particular nemaline myopathy and hypertrophic cardiomyopathy. | |||||||||
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_8165.map.gz | 47.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-8165-v30.xml emd-8165.xml | 21.3 KB 21.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_8165.png | 249 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-8165 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8165 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_8165_validation.pdf.gz | 289.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_8165_full_validation.pdf.gz | 288.4 KB | 表示 | |
XML形式データ | emd_8165_validation.xml.gz | 6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8165 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8165 | 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_8165.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.1 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 : F-actin-myosin-tropomyosin complex
全体 | 名称: F-actin-myosin-tropomyosin complex |
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要素 |
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-超分子 #1: F-actin-myosin-tropomyosin complex
超分子 | 名称: F-actin-myosin-tropomyosin complex / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all / 詳細: Filament |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
-超分子 #2: F-actin
超分子 | 名称: F-actin / タイプ: complex / ID: 2 / 親要素: 1 / 含まれる分子: #1 |
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由来(天然) | 生物種: Dictyostelium discoideum (キイロタマホコリカビ) |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
-超分子 #3: Myosin
超分子 | 名称: Myosin / タイプ: complex / ID: 3 / 親要素: 1 / 含まれる分子: #2 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Escherichia coli (大腸菌) |
-超分子 #4: tropomyosin
超分子 | 名称: tropomyosin / タイプ: complex / ID: 4 / 親要素: 1 / 含まれる分子: #3 |
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-分子 #1: Actin, cytoplasmic 2
分子 | 名称: Actin, cytoplasmic 2 / タイプ: protein_or_peptide / ID: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Dictyostelium discoideum (キイロタマホコリカビ) |
組換発現 | 生物種: Spodoptera frugiperda (ツマジロクサヨトウ) |
配列 | 文字列: EEEIAALVID NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI EHGIVTNWDD MEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT H TVPIYEGY ...文字列: EEEIAALVID NGSGMCKAGF AGDDAPRAVF PSIVGRPRHQ GVMVGMGQKD SYVGDEAQSK RGILTLKYPI EHGIVTNWDD MEKIWHHTF YNELRVAPEE HPVLLTEAPL NPKANREKMT QIMFETFNTP AMYVAIQAVL SLYASGRTTG IVMDSGDGVT H TVPIYEGY ALPHAILRLD LAGRDLTDYL MKILTERGYS FTTTAEREIV RDIKEKLCYV ALDFEQEMAT AASSSSLEKS YE LPDGQVI TIGNERFRCP EALFQPSFLG MESCGIHETT FNSIMKCDVD IRKDLYANTV LSGGTTMYPG IADRMQKEIT ALA PSTMKI KIIAPPERKY SVWIGGSILA SLSTFQQMWI SKQEYDESGP SIVHRKCF |
-分子 #2: NON MUSCLE MYOSIN 2C, ALPHA-ACTININ
分子 | 名称: NON MUSCLE MYOSIN 2C, ALPHA-ACTININ / タイプ: protein_or_peptide / ID: 2 詳細: NON MUSCLE MYOSIN 2C HEAVY CHAIN, MOTOR DOMAIN RESIDUES 1-799 LINKED TO ALPHA-ACTININ 3, REPEATS 1 AND 2 RESIDUES 800-1039 FRAGMENT: UNP Q7Z406-1 RESIDUES 1-799, UNP P05095 RESIDUES 265-502 光学異性体: LEVO / EC番号: ec: 3.6.4.1 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Escherichia coli (大腸菌) |
配列 | 文字列: MAAVTMSVPG RKAPPRPGPV PEAAQPFLFT PRGPSAGGGP GSGTSPQVEW TARRLVWVPS ELHGFEAAAL RDEGEEEAEV ELAESGRRL RLPRDQIQRM NPPKFSKAED MAELTCLNEA SVLHNLRERY YSGLIYTYSG LFCVVINPYK QLPIYTEAIV E MYRGKKRH ...文字列: MAAVTMSVPG RKAPPRPGPV PEAAQPFLFT PRGPSAGGGP GSGTSPQVEW TARRLVWVPS ELHGFEAAAL RDEGEEEAEV ELAESGRRL RLPRDQIQRM NPPKFSKAED MAELTCLNEA SVLHNLRERY YSGLIYTYSG LFCVVINPYK QLPIYTEAIV E MYRGKKRH EVPPHVYAVT EGAYRSMLQD REDQSILCTG ESGAGKTENT KKVIQYLAHV ASSPKGRKEP GVPGELERQL LQ ANPILEA FGNAKTVKND NSSRFGKFIR INFDVAGYIV GANIETYLLE KSRAIRQAKD ECSFHIFYQL LGGAGEQLKA DLL LEPCSH YRFLTNGPSS SPGQERELFQ ETLESLRVLG FSHEEIISML RMVSAVLQFG NIALKRERNT DQATMPDNTA AQKL CRLLG LGVTDFSRAL LTPRIKVGRD YVQKAQTKEQ ADFALEALAK ATYERLFRWL VLRLNRALDR SPRQGASFLG ILDIA GFEI FQLNSFEQLC INYTNEKLQQ LFNHTMFVLE QEEYQREGIP WTFLDFGLDL QPCIDLIERP ANPPGLLALL DEECWF PKA TDKSFVEKVA QEQGGHPKFQ RPRHLRDQAD FSVLHYAGKV DYKANEWLMK NMDPLNDNVA ALLHQSTDRL TAEIWKD VE GIVGLEQVSS LGDGPPGGRP RRGMFRTVGQ LYKESLSRLM ATLSNTNPSF VRCIVPNHEK RAGKLEPRLV LDQLRCNG V LEGIRICRQG FPNRILFQEF RQRYEILTPN AIPKGFMDGK QACEKMIQAL ELDPNLYRVG QSKIFFRAGV LAQLEEERA SEQTKSDYLK RANELVQWIN DKQASLESRD FGDSIESVQS FMNAHKEYKK TEKPPKGQEV SELEAIYNSL QTKLRLIKRE PFVAPAGLT PNEIDSTWSA LEKAEQEHAE ALRIELKRQK KIAVLLQKYN RILKKLENWA TTKSVYLGSN ETGDSITAVQ A KLKNLEAF DGECQSLEGQ SNSDLLSILA QLTELNYNGV PELTERKDTF FAQQWTGVKS SAETYKNTLL AELERLQKIE D |
-分子 #3: Tropomyosin alpha-3 chain
分子 | 名称: Tropomyosin alpha-3 chain / タイプ: protein_or_peptide / ID: 3 詳細: Human TROPOMYSIN WAS USED (UNP P06753-2,TPM3_HUMAN, RESIDUES 62-196). DUE TO THE LIMITED RESOLUTION OF THE CRYO-EM DENSITY IN THE REGION OF TROPOMYOSIN, TROPOMYOSIN HAS BEEN REPRESENTED AS POLY(UNK). 光学異性体: LEVO |
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配列 | 文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) ...文字列: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) |
-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 | filament |
-試料調製
緩衝液 | pH: 7.5 構成要素:
詳細: 5 mM Tris-HCl pH 7.5, 1 mM DTT, 100 mM KCl, and 2 mM MgCl2 | ||||||||||
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糖包埋 | 材質: I | ||||||||||
グリッド | モデル: C-flat-2/1 / 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 | ||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 90 % / 装置: GATAN CRYOPLUNGE 3 詳細: Sample (2 uL of F-actin-tropomyosin solution) was applied to a glow-discharged holey carbon grid, incubated for 20 s and manually blotted from the backside for less than a second with filter ...詳細: Sample (2 uL of F-actin-tropomyosin solution) was applied to a glow-discharged holey carbon grid, incubated for 20 s and manually blotted from the backside for less than a second with filter paper. Afterwards 1.5 uL of myosin solution (3 uM without nucleotide) were added directly on the grid, incubated for 10 s and then manually blotted for 5 s from the backside with filter paper.. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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詳細 | Cs corrected microscope |
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 - 画像ごとのフレーム数: 2-8 / 実像数: 6300 / 平均露光時間: 0.475 sec. / 平均電子線量: 16.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 最大 デフォーカス(補正後): 2.8 µm / 最小 デフォーカス(補正後): 0.7 µm / 照射モード: OTHER / 撮影モード: BRIGHT FIELD / 倍率(公称値): 59000 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
初期モデル |
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精密化 | プロトコル: BACKBONE TRACE / 温度因子: 180 | ||||||
得られたモデル | PDB-5jlh: |