+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 7x0s | ||||||
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タイトル | Human TRiC-tubulin-S3 | ||||||
要素 |
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キーワード | STRUCTURAL PROTEIN | ||||||
機能・相同性 | 機能・相同性情報 odontoblast differentiation / zona pellucida receptor complex / scaRNA localization to Cajal body / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / tubulin complex assembly / BBSome-mediated cargo-targeting to cilium / cytoskeleton-dependent intracellular transport / binding of sperm to zona pellucida ...odontoblast differentiation / zona pellucida receptor complex / scaRNA localization to Cajal body / chaperone mediated protein folding independent of cofactor / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / tubulin complex assembly / BBSome-mediated cargo-targeting to cilium / cytoskeleton-dependent intracellular transport / binding of sperm to zona pellucida / Folding of actin by CCT/TriC / Formation of tubulin folding intermediates by CCT/TriC / positive regulation of telomerase RNA localization to Cajal body / chaperonin-containing T-complex / Prefoldin mediated transfer of substrate to CCT/TriC / GTPase activating protein binding / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / natural killer cell mediated cytotoxicity / intercellular bridge / regulation of synapse organization / pericentriolar material / nuclear envelope lumen / beta-tubulin binding / MHC class I protein binding / Association of TriC/CCT with target proteins during biosynthesis / : / microtubule-based process / chaperone-mediated protein complex assembly / spindle assembly / RHOBTB2 GTPase cycle / heterochromatin / chaperone-mediated protein folding / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / protein folding chaperone / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / positive regulation of telomere maintenance via telomerase / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / AURKA Activation by TPX2 / acrosomal vesicle / cell projection / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / response to virus / cilium / structural constituent of cytoskeleton / mitotic spindle / mRNA 5'-UTR binding / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / G-protein beta-subunit binding / microtubule cytoskeleton / azurophil granule lumen / Regulation of PLK1 Activity at G2/M Transition / unfolded protein binding / melanosome / protein folding / mitotic cell cycle / cell body / Potential therapeutics for SARS / secretory granule lumen / ficolin-1-rich granule lumen / microtubule / cytoskeleton / protein stabilization / cadherin binding / membrane raft / protein domain specific binding / cell division / GTPase activity / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / GTP binding / structural molecule activity / Golgi apparatus / ATP hydrolysis activity / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / metal ion binding / cytoplasm / cytosol 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 | Cong, Y. / Liu, C.X. | ||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Commun Biol / 年: 2023 タイトル: Pathway and mechanism of tubulin folding mediated by TRiC/CCT along its ATPase cycle revealed using cryo-EM. 著者: Caixuan Liu / Mingliang Jin / Shutian Wang / Wenyu Han / Qiaoyu Zhao / Yifan Wang / Cong Xu / Lei Diao / Yue Yin / Chao Peng / Lan Bao / Yanxing Wang / Yao Cong / 要旨: The eukaryotic chaperonin TRiC/CCT assists the folding of about 10% of cytosolic proteins through an ATP-driven conformational cycle, and the essential cytoskeleton protein tubulin is the obligate ...The eukaryotic chaperonin TRiC/CCT assists the folding of about 10% of cytosolic proteins through an ATP-driven conformational cycle, and the essential cytoskeleton protein tubulin is the obligate substrate of TRiC. Here, we present an ensemble of cryo-EM structures of endogenous human TRiC throughout its ATPase cycle, with three of them revealing endogenously engaged tubulin in different folding stages. The open-state TRiC-tubulin-S1 and -S2 maps show extra density corresponding to tubulin in the cis-ring chamber of TRiC. Our structural and XL-MS analyses suggest a gradual upward translocation and stabilization of tubulin within the TRiC chamber accompanying TRiC ring closure. In the closed TRiC-tubulin-S3 map, we capture a near-natively folded tubulin-with the tubulin engaging through its N and C domains mainly with the A and I domains of the CCT3/6/8 subunits through electrostatic and hydrophilic interactions. Moreover, we also show the potential role of TRiC C-terminal tails in substrate stabilization and folding. Our study delineates the pathway and molecular mechanism of TRiC-mediated folding of tubulin along the ATPase cycle of TRiC, and may also inform the design of therapeutic agents targeting TRiC-tubulin interactions. | ||||||
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 | 7x0s.cif.gz | 1.4 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb7x0s.ent.gz | 1.2 MB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 7x0s.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 | 7x0s_validation.pdf.gz | 1.7 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 7x0s_full_validation.pdf.gz | 1.7 MB | 表示 | |
XML形式データ | 7x0s_validation.xml.gz | 199 KB | 表示 | |
CIF形式データ | 7x0s_validation.cif.gz | 307.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/x0/7x0s ftp://data.pdbj.org/pub/pdb/validation_reports/x0/7x0s | HTTPS FTP |
-関連構造データ
関連構造データ | 32923MC 7wz3C 7x0aC 7x0vC 7x3jC 7x3uC 7x6qC 7x7yC 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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1 |
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-要素
-T-complex protein 1 subunit ... , 8種, 16分子 KzJPHOGNEeIMBLAa
#1: タンパク質 | 分子量: 58106.086 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: CCT6A, CCT6 / 細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P40227 #2: タンパク質 | 分子量: 59691.422 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: CCT8 / 細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P50990 #3: タンパク質 | 分子量: 59417.457 Da / 分子数: 2 / Mutation: L290S / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CCT7, CCTH / 細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: Q99832 #4: タンパク質 | 分子量: 60613.855 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: CCT3, CCTG / 細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P49368 #5: タンパク質 | 分子量: 59547.684 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: CCT5, CCTE / 細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P48643 #6: タンパク質 | 分子量: 57996.113 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: CCT4, CCTD / 細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P50991 #7: タンパク質 | 分子量: 57567.141 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: CCT2, CCTB / 細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P78371 #8: タンパク質 | 分子量: 60418.477 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: TCP1, CCT1, CCTA / 細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P17987 |
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-タンパク質 , 1種, 1分子 R
#9: タンパク質 | 分子量: 49717.629 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: TUBB, TUBB5 / 細胞株 (発現宿主): HEK293F / 発現宿主: Homo sapiens (ヒト) / 参照: UniProt: P07437 |
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-非ポリマー , 4種, 64分子
#10: 化合物 | ChemComp-ADP / #11: 化合物 | ChemComp-MG / #12: 化合物 | ChemComp-AF3 / #13: 水 | ChemComp-HOH / | |
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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: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Human TRiC-tubulin-S3 / タイプ: COMPLEX / Entity ID: #1-#9 / 由来: NATURAL |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Homo sapiens (ヒト) / 細胞: HEK293F |
緩衝液 | pH: 7.5 |
緩衝液成分 | 濃度: 50 mM / 名称: sodium Chloride / 式: NaCl |
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): 2500 nm / 最小 デフォーカス(公称値): 800 nm |
撮影 | 電子線照射量: 38 e/Å2 / 検出モード: SUPER-RESOLUTION 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: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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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: 103406 / 対称性のタイプ: POINT |