+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6wsl | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM structure of VASH1-SVBP bound to microtubules | |||||||||
要素 |
| |||||||||
キーワード | PROTEIN BINDING / Microtubule / Posttranslational modification / Detyrosination / Vasohibin | |||||||||
機能・相同性 | 機能・相同性情報 regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / netrin receptor binding / Post-chaperonin tubulin folding pathway / axonemal microtubule / dorsal root ganglion development / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / regulation of cellular senescence ...regulation of metallopeptidase activity / tubulinyl-Tyr carboxypeptidase / tubulin-tyrosine carboxypeptidase / netrin receptor binding / Post-chaperonin tubulin folding pathway / axonemal microtubule / dorsal root ganglion development / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / regulation of cellular senescence / Carboxyterminal post-translational modifications of tubulin / negative regulation of lymphangiogenesis / organelle transport along microtubule / peptidase activator activity / glial cell differentiation / forebrain morphogenesis / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / neuron projection arborization / cytoskeleton-dependent intracellular transport / cerebellar cortex morphogenesis / Formation of tubulin folding intermediates by CCT/TriC / dentate gyrus development / Gap junction assembly / COPI-independent Golgi-to-ER retrograde traffic / pyramidal neuron differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / Hedgehog 'off' state / Assembly and cell surface presentation of NMDA receptors / centrosome cycle / motor behavior / negative regulation of endothelial cell migration / COPI-dependent Golgi-to-ER retrograde traffic / labyrinthine layer blood vessel development / response to L-glutamate / smoothened signaling pathway / intercellular bridge / regulation of synapse organization / axon development / startle response / negative regulation of endothelial cell proliferation / locomotory exploration behavior / Recycling pathway of L1 / microtubule polymerization / microtubule-based process / negative regulation of blood vessel endothelial cell migration / protein secretion / RHO GTPases activate IQGAPs / response to tumor necrosis factor / regulation of angiogenesis / response to mechanical stimulus / COPI-mediated anterograde transport / metallocarboxypeptidase activity / Activation of AMPK downstream of NMDARs / condensed chromosome / 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 / homeostasis of number of cells within a tissue / negative regulation of protein ubiquitination / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / Resolution of Sister Chromatid Cohesion / cellular response to calcium ion / AURKA Activation by TPX2 / negative regulation of angiogenesis / adult locomotory behavior / filopodium / axon guidance / cell periphery / Translocation of SLC2A4 (GLUT4) to the plasma membrane / intracellular protein transport / RHO GTPases Activate Formins / peptide binding / neuron migration / synapse organization / visual learning / neuromuscular junction / PKR-mediated signaling / recycling endosome / cerebral cortex development / mitotic spindle / structural constituent of cytoskeleton / memory / microtubule cytoskeleton organization / response to wounding / Aggrephagy / HCMV Early Events / cytoplasmic ribonucleoprotein granule / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / 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 / lamellipodium 類似検索 - 分子機能 | |||||||||
生物種 | 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: 3.1 Å | |||||||||
データ登録者 | Li, F. / Li, Y. / Yu, H. | |||||||||
資金援助 | 米国, 2件
| |||||||||
引用 | ジャーナル: Elife / 年: 2020 タイトル: Cryo-EM structure of VASH1-SVBP bound to microtubules. 著者: Faxiang Li / Yang Li / Xuecheng Ye / Haishan Gao / Zhubing Shi / Xuelian Luo / Luke M Rice / Hongtao Yu / 要旨: The dynamic tyrosination-detyrosination cycle of α-tubulin regulates microtubule functions. Perturbation of this cycle impairs mitosis, neural physiology, and cardiomyocyte contraction. The ...The dynamic tyrosination-detyrosination cycle of α-tubulin regulates microtubule functions. Perturbation of this cycle impairs mitosis, neural physiology, and cardiomyocyte contraction. The carboxypeptidases vasohibins 1 and 2 (VASH1 and VASH2), in complex with the small vasohibin-binding protein (SVBP), mediate α-tubulin detyrosination. These enzymes detyrosinate microtubules more efficiently than soluble αβ-tubulin heterodimers. The structural basis for this substrate preference is not understood. Using cryo-electron microscopy (cryo-EM), we have determined the structure of human VASH1-SVBP bound to microtubules. The acidic C-terminal tail of α-tubulin binds to a positively charged groove near the active site of VASH1. VASH1 forms multiple additional contacts with the globular domain of α-tubulin, including contacts with a second α-tubulin in an adjacent protofilament. Simultaneous engagement of two protofilaments by VASH1 can only occur within the microtubule lattice, but not with free αβ heterodimers. These lattice-specific interactions enable preferential detyrosination of microtubules by VASH1. | |||||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6wsl.cif.gz | 445 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb6wsl.ent.gz | 358.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6wsl.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 | 6wsl_validation.pdf.gz | 1.2 MB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 6wsl_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | 6wsl_validation.xml.gz | 61.7 KB | 表示 | |
CIF形式データ | 6wsl_validation.cif.gz | 93.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ws/6wsl ftp://data.pdbj.org/pub/pdb/validation_reports/ws/6wsl | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
|
-要素
-タンパク質 , 4種, 8分子 AEBFCGDH
#1: タンパク質 | 分子量: 50188.441 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TUBA1A, TUBA3 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q71U36 #2: タンパク質 | 分子量: 50481.520 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TUBB3, TUBB4 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q13509 #3: タンパク質 | 分子量: 29780.445 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: VASH1, KIAA1036, VASH / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q7L8A9, tubulinyl-Tyr carboxypeptidase #4: タンパク質 | 分子量: 7821.939 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: SVBP, CCDC23 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q8N300 |
---|
-非ポリマー , 2種, 4分子
#5: 化合物 | #6: 化合物 | |
---|
-詳細
研究の焦点であるリガンドがあるか | N |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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: Tenary complex of microtubule with VASH1-SVBP complex タイプ: COMPLEX / Entity ID: #1-#4 / 由来: MULTIPLE SOURCES |
---|---|
由来(天然) | 生物種: Homo sapiens (ヒト) |
緩衝液 | pH: 7.5 |
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 / 湿度: 95 % / 凍結前の試料温度: 86 K |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
---|---|
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 |
撮影 | 電子線照射量: 50 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
-解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
3次元再構成 | 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 46999 / 対称性のタイプ: POINT |