+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8ixa | ||||||
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タイトル | GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin non-seam region | ||||||
要素 |
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キーワード | STRUCTURAL PROTEIN / microtubule / tubulin isotype / cryo-EM structure | ||||||
機能・相同性 | 機能・相同性情報 Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / cytoplasm organization / cytolytic granule membrane / COPI-independent Golgi-to-ER retrograde traffic / plus-end-directed vesicle transport along microtubule / mitocytosis ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / cytoplasm organization / cytolytic granule membrane / COPI-independent Golgi-to-ER retrograde traffic / plus-end-directed vesicle transport along microtubule / mitocytosis / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / anterograde dendritic transport of neurotransmitter receptor complex / PKR-mediated signaling / Aggrephagy / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases activate IQGAPs / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / The role of GTSE1 in G2/M progression after G2 checkpoint / retrograde neuronal dense core vesicle transport / Recycling pathway of L1 / axonemal microtubule / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases Activate Formins / Separation of Sister Chromatids / Hedgehog 'off' state / organelle transport along microtubule / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / glial cell differentiation / AURKA Activation by TPX2 / vesicle transport along microtubule / forebrain morphogenesis / neuron projection arborization / Regulation of PLK1 Activity at G2/M Transition / lysosome localization / cerebellar cortex morphogenesis / positive regulation of potassium ion transport / dentate gyrus development / MHC class II antigen presentation / pyramidal neuron differentiation / plus-end-directed microtubule motor activity / Kinesins / RHO GTPases activate KTN1 / stress granule disassembly / centrosome cycle / natural killer cell mediated cytotoxicity / motor behavior / mitochondrion transport along microtubule / ciliary rootlet / COPI-dependent Golgi-to-ER retrograde traffic / centrosome localization / microtubule motor activity / response to L-glutamate / kinesin complex / synaptic vesicle transport / adult behavior / smoothened signaling pathway / intercellular bridge / regulation of synapse organization / Insulin processing / microtubule-based movement / startle response / locomotory exploration behavior / cytoplasmic microtubule / microtubule polymerization / centriolar satellite / response to tumor necrosis factor / response to mechanical stimulus / condensed chromosome / homeostasis of number of cells within a tissue / axon cytoplasm / phagocytic vesicle / cellular response to calcium ion / MHC class II antigen presentation / dendrite cytoplasm / adult locomotory behavior / neurogenesis / regulation of membrane potential / locomotory behavior / axon guidance / positive regulation of synaptic transmission, GABAergic / hippocampus development / positive regulation of protein localization to plasma membrane / synapse organization / 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 / intracellular protein transport / neuron migration / visual learning / neuromuscular junction / recycling endosome / neuron differentiation / structural constituent of cytoskeleton 類似検索 - 分子機能 | ||||||
生物種 | Mus musculus (ハツカネズミ) Homo sapiens (ヒト) | ||||||
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: 4.2 Å | ||||||
データ登録者 | Zheng, W. / Zhao, Q.Y. / Diao, L. / Bao, L. / Cong, Y. | ||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Acta Biochim Biophys Sin (Shanghai) / 年: 2023 タイトル: Cryo-EM of α-tubulin isotype-containing microtubules revealed a contracted structure of α4A/β2A microtubules. 著者: Lei Diao / Wei Zheng / Qiaoyu Zhao / Mingyi Liu / Zhenglin Fu / Xu Zhang / Lan Bao / Yao Cong / 要旨: Microtubules are hollow α/β-tubulin heterodimeric polymers that play critical roles in cells. In vertebrates, both α- and β-tubulins have multiple isotypes encoded by different genes, which are ...Microtubules are hollow α/β-tubulin heterodimeric polymers that play critical roles in cells. In vertebrates, both α- and β-tubulins have multiple isotypes encoded by different genes, which are intrinsic factors in regulating microtubule functions. However, the structures of microtubules composed of different tubulin isotypes, especially α-tubulin isotypes, remain largely unknown. Here, we purify recombinant tubulin heterodimers composed of different mouse α-tubulin isotypes, including α1A, α1C and α4A, with the β-tubulin isotype β2A. We further assemble and determine the cryo-electron microscopy (cryo-EM) structures of α1A/β2A, α1C/β2A, and α4A/β2A microtubules. Our structural analysis demonstrates that α4A/β2A microtubules exhibit longitudinal contraction between tubulin interdimers compared with α1A/β2A and α1C/β2A microtubules. Collectively, our findings reveal that α-tubulin isotype composition can tune microtubule structures, and also provide evidence for the "tubulin code" hypothesis. | ||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8ixa.cif.gz | 1.8 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8ixa.ent.gz | 1.5 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8ixa.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 8ixa_validation.pdf.gz | 2.9 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 8ixa_full_validation.pdf.gz | 3 MB | 表示 | |
XML形式データ | 8ixa_validation.xml.gz | 262.8 KB | 表示 | |
CIF形式データ | 8ixa_validation.cif.gz | 393.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ix/8ixa ftp://data.pdbj.org/pub/pdb/validation_reports/ix/8ixa | HTTPS FTP |
-関連構造データ
関連構造データ | 35790MC 8ixbC 8ixdC 8ixeC 8ixfC 8ixgC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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-要素
-タンパク質 , 3種, 27分子 IABCDEFGHQJKLMNOPRYSTUVWXZa
#1: タンパク質 | 分子量: 51017.320 Da / 分子数: 9 / 由来タイプ: 組換発現 詳細: Author stated: the data processing is a non-standard procedure for microtubule-type of helical reconstruction with a seam, and it was performed around 2017 to 2019. We followed the procedure ...詳細: Author stated: the data processing is a non-standard procedure for microtubule-type of helical reconstruction with a seam, and it was performed around 2017 to 2019. We followed the procedure developed by Dr. Rui Zhang (R. Zhang, Cell, 2015, doi: 10.1016/j.cell.2015.07.012), with all the scripts provided by him. In this way, the generated half-maps have an applied circular mask but without touching the structural outer boundaries. 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Tuba1a, Tuba1 / 発現宿主: Insecta environmental sample (昆虫) 参照: UniProt: P68369, 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 #2: タンパク質 | 分子量: 51150.961 Da / 分子数: 9 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 遺伝子: Tubb2a, Tubb2 / 発現宿主: Insecta environmental sample (昆虫) / 参照: UniProt: Q7TMM9 #3: タンパク質 | 分子量: 41721.066 Da / 分子数: 9 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: KIF5B, KNS, KNS1 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: P33176 |
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-非ポリマー , 3種, 27分子
#4: 化合物 | ChemComp-GTP / #5: 化合物 | ChemComp-G2P / #6: 化合物 | ChemComp-ATP / |
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-詳細
研究の焦点であるリガンドがあるか | N |
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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 |
-試料調製
構成要素 | 名称: GMPCPP-Alpha1A/Beta2A-microtubule decorated with kinesin タイプ: COMPLEX / Entity ID: #1-#3 / 由来: RECOMBINANT |
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由来(天然) | 生物種: Mus musculus (ハツカネズミ) |
由来(組換発現) | 生物種: Insecta environmental sample (昆虫) |
緩衝液 | pH: 6.9 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 1500 nm / 最小 デフォーカス(公称値): 800 nm |
撮影 | 電子線照射量: 36 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) |
-解析
CTF補正 | タイプ: NONE |
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3次元再構成 | 解像度: 4.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 19287 / 対称性のタイプ: POINT |