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基本情報
登録情報 | データベース: EMDB / ID: EMD-21893 | |||||||||
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タイトル | Cryo-EM structure of VASH1-SVBP bound to microtubules | |||||||||
![]() | Cryo-EM structure of VASH1-SVBP bound to microtubules | |||||||||
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![]() | Microtubule / Posttranslational modification / Detyrosination / Vasohibin / PROTEIN BINDING | |||||||||
機能・相同性 | ![]() 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 / Gap junction assembly / dentate gyrus development / COPI-independent Golgi-to-ER retrograde traffic / pyramidal neuron differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / Assembly and cell surface presentation of NMDA receptors / Kinesins / centrosome cycle / motor behavior / negative regulation of endothelial cell migration / labyrinthine layer blood vessel development / COPI-dependent Golgi-to-ER retrograde traffic / response to L-glutamate / smoothened signaling pathway / intercellular bridge / regulation of synapse organization / axon development / startle response / locomotory exploration behavior / negative regulation of endothelial cell proliferation / 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 / Hedgehog 'off' state / COPI-mediated anterograde transport / metallocarboxypeptidase activity / Activation of AMPK downstream of NMDARs / response to mechanical stimulus / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / condensed chromosome / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / homeostasis of number of cells within a tissue / Recruitment of mitotic centrosome proteins and complexes / negative regulation of protein ubiquitination / 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 / cellular response to calcium ion / MHC class II antigen presentation / AURKA Activation by TPX2 / negative regulation of angiogenesis / adult locomotory behavior / filopodium / axon guidance / cell periphery / 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 / intracellular protein transport / synapse organization / neuron migration / peptide binding / cell cycle / visual learning / neuromuscular junction / PKR-mediated signaling / recycling endosome / structural constituent of cytoskeleton / mitotic spindle / memory / cerebral cortex development / response to wounding / microtubule cytoskeleton organization / 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 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.1 Å | |||||||||
![]() | Li F / Li Y | |||||||||
資金援助 | ![]()
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![]() | ![]() 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 |
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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
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マップデータ | ![]() | 95.1 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 14.1 KB 14.1 KB | 表示 表示 | ![]() |
画像 | ![]() | 118 KB | ||
Filedesc metadata | ![]() | 6 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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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 | Cryo-EM structure of VASH1-SVBP bound to microtubules | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.83 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 : Tenary complex of microtubule with VASH1-SVBP complex
全体 | 名称: Tenary complex of microtubule with VASH1-SVBP complex |
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要素 |
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-超分子 #1: Tenary complex of microtubule with VASH1-SVBP complex
超分子 | 名称: Tenary complex of microtubule with VASH1-SVBP complex タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#4 |
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由来(天然) | 生物種: ![]() |
-分子 #1: Tubulin alpha-1A chain
分子 | 名称: Tubulin alpha-1A chain / タイプ: protein_or_peptide / ID: 1 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 50.188441 KDa |
組換発現 | 生物種: ![]() |
配列 | 文字列: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE ...文字列: MRECISIHVG QAGVQIGNAC WELYCLEHGI QPDGQMPSDK TIGGGDDSFN TFFSETGAGK HVPRAVFVDL EPTVIDEVRT GTYRQLFHP EQLITGKEDA ANNYARGHYT IGKEIIDLVL DRIRKLADQC TGLQGFLVFH SFGGGTGSGF TSLLMERLSV D YGKKSKLE FSIYPAPQVS TAVVEPYNSI LTTHTTLEHS DCAFMVDNEA IYDICRRNLD IERPTYTNLN RLIGQIVSSI TA SLRFDGA LNVDLTEFQT NLVPYPRIHF PLATYAPVIS AEKAYHEQLS VAEITNACFE PANQMVKCDP RHGKYMACCL LYR GDVVPK DVNAAIATIK TKRTIQFVDW CPTGFKVGIN YQPPTVVPGG DLAKVQRAVC MLSNTTAIAE AWARLDHKFD LMYA KRAFV HWYVGEGMEE GEFSEAREDM AALEKDYEEV GVDSVEGEGE EEGEEY UniProtKB: Tubulin alpha-1A chain |
-分子 #2: Tubulin beta-3 chain
分子 | 名称: Tubulin beta-3 chain / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 50.48152 KDa |
組換発現 | 生物種: ![]() |
配列 | 文字列: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPSGNYVGDS DLQLERISVY YNEASSHKYV PRAILVDLEP GTMDSVRSGA FGHLFRPDN FIFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKECENCDC LQGFQLTHSL GGGTGSGMGT LLISKVREEY P DRIMNTFS ...文字列: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPSGNYVGDS DLQLERISVY YNEASSHKYV PRAILVDLEP GTMDSVRSGA FGHLFRPDN FIFGQSGAGN NWAKGHYTEG AELVDSVLDV VRKECENCDC LQGFQLTHSL GGGTGSGMGT LLISKVREEY P DRIMNTFS VVPSPKVSDT VVEPYNATLS IHQLVENTDE TYCIDNEALY DICFRTLKLA TPTYGDLNHL VSATMSGVTT SL RFPGQLN ADLRKLAVNM VPFPRLHFFM PGFAPLTARG SQQYRALTVP ELTQQMFDAK NMMAACDPRH GRYLTVATVF RGR MSMKEV DEQMLAIQSK NSSYFVEWIP NNVKVAVCDI PPRGLKMSST FIGNSTAIQE LFKRISEQFT AMFRRKAFLH WYTG EGMDE MEFTEAESNM NDLVSEYQQY QDATAEEEGE MYEDDEEESE AQGPK UniProtKB: Tubulin beta-3 chain |
-分子 #3: Tubulinyl-Tyr carboxypeptidase 1
分子 | 名称: Tubulinyl-Tyr carboxypeptidase 1 / タイプ: protein_or_peptide / ID: 3 / コピー数: 2 / 光学異性体: LEVO / EC番号: tubulinyl-Tyr carboxypeptidase |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 29.780445 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: DLRDGGVPFF VNRGGLPVDE ATWERMWKHV AKIHPDGEKV AQRIRGATDL PKIPIPSVPT FQPSTPVPER LEAVQRYIRE LQYNHTGTQ FFEIKKSRPL TGLMDLAKEM TKEALPIKCL EAVILGIYLT NSMPTLERFP ISFKTYFSGN YFRHIVLGVN F AGRYGALG ...文字列: DLRDGGVPFF VNRGGLPVDE ATWERMWKHV AKIHPDGEKV AQRIRGATDL PKIPIPSVPT FQPSTPVPER LEAVQRYIRE LQYNHTGTQ FFEIKKSRPL TGLMDLAKEM TKEALPIKCL EAVILGIYLT NSMPTLERFP ISFKTYFSGN YFRHIVLGVN F AGRYGALG MSRREDLMYK PPAFRTLSEL VLDFEAAYGR CWHVLKKVKL GQSVSHDPHS VEQIEWKHSV LDVERLGRDD FR KELERHA RDMRLKIGKG TG UniProtKB: Tubulinyl-Tyr carboxypeptidase 1 |
-分子 #4: Small vasohibin-binding protein
分子 | 名称: Small vasohibin-binding protein / タイプ: protein_or_peptide / ID: 4 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 7.821939 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MDPPARKEKT KVKESVSRVE KAKQKSAQQE LKQRQRAEIY ALNRVMTELE QQQFDEFCKQ MQPPGE UniProtKB: Small vasohibin-binding protein |
-分子 #5: GUANOSINE-5'-TRIPHOSPHATE
分子 | 名称: GUANOSINE-5'-TRIPHOSPHATE / タイプ: ligand / ID: 5 / コピー数: 2 / 式: GTP |
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分子量 | 理論値: 523.18 Da |
Chemical component information | ![]() ChemComp-GTP: |
-分子 #6: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
分子 | 名称: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER / タイプ: ligand / ID: 6 / コピー数: 2 / 式: G2P |
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分子量 | 理論値: 521.208 Da |
Chemical component information | ![]() ChemComp-G2P: |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | filament |
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試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 86 K |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
初期モデル | モデルのタイプ: EMDB MAP |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 46999 |
初期 角度割当 | タイプ: ANGULAR RECONSTITUTION |
最終 角度割当 | タイプ: ANGULAR RECONSTITUTION |