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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-6352 | |||||||||
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タイトル | Cryo-EM structure of GMPCPP-microtubule (14 protofilaments) decorated with kinesin | |||||||||
![]() | 3D reconstruction of kinesin-bound GMPCPP microtubule (14 protofilaments) with pseudo-helical symmetry imposed | |||||||||
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![]() | microtubule / GMPCPP / kinesin | |||||||||
機能・相同性 | ![]() Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / mitotic cell cycle / microtubule / GTPase activity / GTP binding / metal ion binding / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() | |||||||||
手法 | らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 3.5 Å | |||||||||
![]() | Zhang R / Alushin GM / Brown A / Nogales E | |||||||||
![]() | ![]() タイトル: Mechanistic Origin of Microtubule Dynamic Instability and Its Modulation by EB Proteins. 著者: Rui Zhang / Gregory M Alushin / Alan Brown / Eva Nogales / ![]() ![]() 要旨: Microtubule (MT) dynamic instability is driven by GTP hydrolysis and regulated by microtubule-associated proteins, including the plus-end tracking end-binding protein (EB) family. We report six cryo- ...Microtubule (MT) dynamic instability is driven by GTP hydrolysis and regulated by microtubule-associated proteins, including the plus-end tracking end-binding protein (EB) family. We report six cryo-electron microscopy (cryo-EM) structures of MTs, at 3.5 Å or better resolution, bound to GMPCPP, GTPγS, or GDP, either decorated with kinesin motor domain after polymerization or copolymerized with EB3. Subtle changes around the E-site nucleotide during hydrolysis trigger conformational changes in α-tubulin around an "anchor point," leading to global lattice rearrangements and strain generation. Unlike the extended lattice of the GMPCPP-MT, the EB3-bound GTPγS-MT has a compacted lattice that differs in lattice twist from that of the also compacted GDP-MT. These results and the observation that EB3 promotes rapid hydrolysis of GMPCPP suggest that EB proteins modulate structural transitions at growing MT ends by recognizing and promoting an intermediate state generated during GTP hydrolysis. Our findings explain both EBs end-tracking behavior and their effect on microtubule dynamics. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 155.9 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 12.9 KB 12.9 KB | 表示 表示 | ![]() |
画像 | ![]() ![]() | 165.8 KB 8.1 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 3jatMC ![]() 6347C ![]() 6348C ![]() 6349C ![]() 6350C ![]() 6351C ![]() 6353C ![]() 6354C ![]() 6355C ![]() 3jakC ![]() 3jalC ![]() 3jarC ![]() 3jasC ![]() 3jawC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ |
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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 | 3D reconstruction of kinesin-bound GMPCPP microtubule (14 protofilaments) with pseudo-helical symmetry imposed | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.32 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
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試料の構成要素
-全体 : kinesin-bound GMPCPP microtubule
全体 | 名称: kinesin-bound GMPCPP microtubule |
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要素 |
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-超分子 #1000: kinesin-bound GMPCPP microtubule
超分子 | 名称: kinesin-bound GMPCPP microtubule / タイプ: sample / ID: 1000 / 集合状態: helical assembly / Number unique components: 3 |
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-分子 #1: Alpha tubulin
分子 | 名称: Alpha tubulin / タイプ: protein_or_peptide / ID: 1 詳細: Porcine tubulin powder was purchased from Cytoskeleton Inc. 集合状態: Helical assembly / 組換発現: No / データベース: NCBI |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 55 KDa |
配列 | UniProtKB: Tubulin alpha-1B chain |
-分子 #2: Beta tubulin
分子 | 名称: Beta tubulin / タイプ: protein_or_peptide / ID: 2 詳細: Porcine tubulin powder was purchased from Cytoskeleton Inc. 集合状態: Helical assembly / 組換発現: No / データベース: NCBI |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 55 KDa |
配列 | UniProtKB: Tubulin beta chain |
-分子 #3: kinesin
分子 | 名称: kinesin / タイプ: protein_or_peptide / ID: 3 詳細: Human monomeric kinesin K349 cys-lite described in: Rice, S., Lin, A.W., Safer, D., Hart, C.L., Naber, N., Carragher, B.O., Cain, S.M., Pechatnikova, E., Wilson-Kubalek, E.M., Whittaker, M., ...詳細: Human monomeric kinesin K349 cys-lite described in: Rice, S., Lin, A.W., Safer, D., Hart, C.L., Naber, N., Carragher, B.O., Cain, S.M., Pechatnikova, E., Wilson-Kubalek, E.M., Whittaker, M., et al. (1999). A structural change in the kinesin motor protein that drives motility. Nature 402, 778-784. 集合状態: monomer / 組換発現: Yes |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 36 KDa |
組換発現 | 生物種: ![]() ![]() |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | らせん対称体再構成法 |
試料の集合状態 | helical array |
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試料調製
濃度 | 3 mg/mL |
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緩衝液 | pH: 6.8 詳細: 80 mM PIPES, 1 mM EGTA, 1 mM MgCl2, 1 mM DTT, 0.05% Nonidet P-40 |
グリッド | 詳細: 400 mesh C-flat 1.2/1.3 EM grid, glow discharged in Ar/O2 gas (Solarus, Gatan Inc) |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 90.4 K / 装置: FEI VITROBOT MARK II / 手法: Blot once for 4 seconds before plunging. |
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電子顕微鏡法
顕微鏡 | FEI TITAN |
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温度 | 平均: 90 K |
アライメント法 | Legacy - 非点収差: Objective lens astigmatism was corrected at 27,500 times magnification. |
詳細 | The camera was operated in counting mode, with a dose rate of ~8 electrons/pixel/s on the camera. A total exposure time of 6 s was fractionated into 20 movie frames. |
日付 | 2014年3月2日 |
撮影 | カテゴリ: CCD / フィルム・検出器のモデル: GATAN K2 (4k x 4k) / 実像数: 695 / 平均電子線量: 27.6 e/Å2 詳細: The camera was operated in counting mode, with a dose rate of ~8 electrons/pixel/s on the camera. A total exposure time of 6 s was fractionated into 20 movie frames. |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 27500 / 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): 3.5 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 27500 |
試料ステージ | 試料ホルダー: Gatan 626 holder / 試料ホルダーモデル: GATAN LIQUID NITROGEN |
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画像解析
詳細 | IHRSR algorithm with microtubule-specific pseudo-helical symmetry applied |
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最終 再構成 | 想定した対称性 - らせんパラメータ - Δz: 8.92 Å 想定した対称性 - らせんパラメータ - ΔΦ: 25.75 ° 想定した対称性 - らせんパラメータ - 軸対称性: C1 (非対称) アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 3.5 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: EMAN1, FREALIGN 詳細: Pseudo-helical symmetry was applied during the reconstruction step. |
CTF補正 | 詳細: CTFFIND4, each particle |