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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: PDB / ID: 8t42 | ||||||
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タイトル | Model of TTLL6 MTBH1-2 bound to microtubule | ||||||
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![]() | LIGASE / tubulin post-translational modifications / microtubules / TTLL | ||||||
機能・相同性 | ![]() positive regulation of cilium movement / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / 9+0 non-motile cilium / microtubule severing / regulation of cilium beat frequency involved in ciliary motility / 合成酵素; C-N結合を形成; 酸-D-アミノ酸リガーゼ(ペプチド合成) / odontoblast differentiation ...positive regulation of cilium movement / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / 9+0 non-motile cilium / microtubule severing / regulation of cilium beat frequency involved in ciliary motility / 合成酵素; C-N結合を形成; 酸-D-アミノ酸リガーゼ(ペプチド合成) / odontoblast differentiation / Post-chaperonin tubulin folding pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / cytoskeleton-dependent intracellular transport / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / COPI-independent Golgi-to-ER retrograde traffic / microtubule bundle formation / Assembly and cell surface presentation of NMDA receptors / Kinesins / GTPase activating protein binding / COPI-dependent Golgi-to-ER retrograde traffic / natural killer cell mediated cytotoxicity / intercellular bridge / regulation of synapse organization / nuclear envelope lumen / cytoplasmic microtubule / MHC class I protein binding / Recycling pathway of L1 / microtubule-based process / RHOH GTPase cycle / RHO GTPases activate IQGAPs / spindle assembly / cellular response to interleukin-4 / Hedgehog 'off' state / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / 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 / tubulin binding / AURKA Activation by TPX2 / ciliary basal body / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / 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 / HCMV Early Events / PKR-mediated signaling / cilium / structural constituent of cytoskeleton / mitotic spindle / microtubule cytoskeleton organization / Aggrephagy / cytoplasmic ribonucleoprotein granule / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / double-stranded RNA binding / mitotic cell cycle / cell body / Potential therapeutics for SARS / microtubule / cytoskeleton / membrane raft / protein domain specific binding / cell division / GTPase activity / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / GTP binding / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | ||||||
生物種 | ![]() ![]() ![]() | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å | ||||||
![]() | Mahalingan, K.K. / Grotjahn, D. / Li, Y. / Lander, G.C. / Zehr, E.A. / Roll-Mecak, A. | ||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural basis for α-tubulin-specific and modification state-dependent glutamylation. 著者: Kishore K Mahalingan / Danielle A Grotjahn / Yan Li / Gabriel C Lander / Elena A Zehr / Antonina Roll-Mecak / ![]() 要旨: Microtubules have spatiotemporally complex posttranslational modification patterns. Tubulin tyrosine ligase-like (TTLL) enzymes introduce the most prevalent modifications on α-tubulin and β-tubulin. ...Microtubules have spatiotemporally complex posttranslational modification patterns. Tubulin tyrosine ligase-like (TTLL) enzymes introduce the most prevalent modifications on α-tubulin and β-tubulin. How TTLLs specialize for specific substrate recognition and ultimately modification-pattern generation is largely unknown. TTLL6, a glutamylase implicated in ciliopathies, preferentially modifies tubulin α-tails in microtubules. Cryo-electron microscopy, kinetic analysis and single-molecule biochemistry reveal an unprecedented quadrivalent recognition that ensures simultaneous readout of microtubule geometry and posttranslational modification status. By binding to a β-tubulin subunit, TTLL6 modifies the α-tail of the longitudinally adjacent tubulin dimer. Spanning two tubulin dimers along and across protofilaments (PFs) ensures fidelity of recognition of both the α-tail and the microtubule. Moreover, TTLL6 reads out and is stimulated by glutamylation of the β-tail of the laterally adjacent tubulin dimer, mediating crosstalk between α-tail and β-tail. This positive feedback loop can generate localized microtubule glutamylation patterns. Our work uncovers general principles that generate tubulin chemical and topographic complexity. | ||||||
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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PDBx/mmCIF形式 | ![]() | 322.6 KB | 表示 | ![]() |
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PDB形式 | ![]() | 254.5 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 1.3 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.3 MB | 表示 | |
XML形式データ | ![]() | 70.3 KB | 表示 | |
CIF形式データ | ![]() | 105.4 KB | 表示 | |
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 | ![]() 41018MC ![]() 8u3zC C: 同じ文献を引用 ( M: このデータのモデリングに利用したマップデータ |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
実験データセット #1 | データ参照: ![]() 詳細: Cryo-EM micrographs of human alpha1B/BetaI+BetaIVb microtubules bound to GMPCPP decorated with TTLL6 Metadata reference: 10.6019/EMPIAR-11798 |
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リンク
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集合体
登録構造単位 | ![]()
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要素
-タンパク質 , 3種, 5分子 AFBEN
#1: タンパク質 | 分子量: 50204.445 Da / 分子数: 2 / 由来タイプ: 天然 / 詳細: a-tubulin from tsA201 cell line / 由来: (天然) ![]() #2: タンパク質 | 分子量: 49717.629 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) ![]() #3: タンパク質 | | 分子量: 59145.621 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) ![]() ![]() ![]() ![]() 参照: UniProt: A4Q9E8, 合成酵素; C-N結合を形成; 酸-D-アミノ酸リガーゼ(ペプチド合成) |
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-非ポリマー , 3種, 8分子 ![](data/chem/img/GTP.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/G2P.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/G2P.gif)
#4: 化合物 | #5: 化合物 | ChemComp-MG / #6: 化合物 | |
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-詳細
研究の焦点であるリガンドがあるか | Y |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: FILAMENT / 3次元再構成法: 単粒子再構成法 |
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試料調製
構成要素 |
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分子量 | 値: 0.3 MDa / 実験値: YES | ||||||||||||||||||||||||||||||
由来(天然) |
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由来(組換発現) | 生物種: ![]() ![]() | ||||||||||||||||||||||||||||||
緩衝液 | pH: 7 | ||||||||||||||||||||||||||||||
緩衝液成分 |
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試料 | 濃度: 0.1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: TTLL6 decoration of microtubule was heterogenous | ||||||||||||||||||||||||||||||
試料支持 | グリッドの材料: GOLD / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 303 K 詳細: The sample was blotted with Whatman #5 blotting paper on both sides of the grid for 3 s with a blot offset of -1 using a Vitrobot Mark IV (Thermo Fisher Scientific) with a chamber set to 30C ...詳細: The sample was blotted with Whatman #5 blotting paper on both sides of the grid for 3 s with a blot offset of -1 using a Vitrobot Mark IV (Thermo Fisher Scientific) with a chamber set to 30C at 100% humidity and subsequently plunged into liquid ethane. |
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電子顕微鏡撮影
実験機器 | ![]() モデル: Talos Arctica / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TALOS ARCTICA |
電子銃 | 電子線源: ![]() |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 36000 X / 最大 デフォーカス(公称値): 2000 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm / アライメント法: COMA FREE |
撮影 | 平均露光時間: 9.75 sec. / 電子線照射量: 42 e/Å2 / 検出モード: COUNTING フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 実像数: 2771 |
画像スキャン | 動画フレーム数/画像: 39 / 利用したフレーム数/画像: 1-39 |
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解析
EMソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / カテゴリ: モデル精密化 | ||||||||||||||||||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 59044 詳細: Due to highly heterogeneous TTLL6 decoration of microtubules microtubules were manually selected. 59044 overlapping segments with a box size of 568 pixels were extracted every 82 A | ||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 392289 / アルゴリズム: FOURIER SPACE / クラス平均像の数: 1 / 対称性のタイプ: POINT | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL / Target criteria: Cross-correlation | ||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | 3D fitting-ID: 1
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拘束条件 |
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