+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-35122 | |||||||||
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タイトル | Human TRiC-PhLP2A complex in the closed state | |||||||||
マップデータ | A primary EM map | |||||||||
試料 |
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キーワード | chaperonin complex / CHAPERONE / cochaperone | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of chaperone-mediated protein folding / perinucleolar compartment / scaRNA localization to Cajal body / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / chaperone mediated protein folding independent of cofactor / tubulin complex assembly / BBSome-mediated cargo-targeting to cilium / binding of sperm to zona pellucida ...negative regulation of chaperone-mediated protein folding / perinucleolar compartment / scaRNA localization to Cajal body / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / positive regulation of protein localization to Cajal body / chaperone mediated protein folding independent of cofactor / tubulin complex assembly / BBSome-mediated cargo-targeting to cilium / binding of sperm to zona pellucida / positive regulation of telomerase RNA localization to Cajal body / Folding of actin by CCT/TriC / Formation of tubulin folding intermediates by CCT/TriC / vascular endothelial growth factor receptor 2 binding / chaperonin-containing T-complex / Prefoldin mediated transfer of substrate to CCT/TriC / RHOBTB1 GTPase cycle / intermediate filament cytoskeleton / WD40-repeat domain binding / pericentriolar material / beta-tubulin binding / Association of TriC/CCT with target proteins during biosynthesis / : / chaperone-mediated protein complex assembly / RHOBTB2 GTPase cycle / heterochromatin / negative regulation of ubiquitin-dependent protein catabolic process / regulation of peptidyl-tyrosine phosphorylation / chaperone-mediated protein folding / protein folding chaperone / positive regulation of telomere maintenance via telomerase / positive regulation of endothelial cell proliferation / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / acrosomal vesicle / cell projection / mRNA 3'-UTR binding / ATP-dependent protein folding chaperone / response to virus / cilium / mRNA 5'-UTR binding / positive regulation of angiogenesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / azurophil granule lumen / G-protein beta-subunit binding / unfolded protein binding / melanosome / protein folding / actin cytoskeleton organization / cell body / angiogenesis / secretory granule lumen / ficolin-1-rich granule lumen / microtubule / cytoskeleton / protein stabilization / cadherin binding / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / apoptotic process / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / RNA binding / extracellular exosome / extracellular region / nucleoplasm / ATP binding / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.24 Å | |||||||||
データ登録者 | Roh SH / Park J / Kim H / Lim S | |||||||||
資金援助 | 韓国, 1件
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引用 | ジャーナル: Nat Commun / 年: 2024 タイトル: A structural vista of phosducin-like PhLP2A-chaperonin TRiC cooperation during the ATP-driven folding cycle. 著者: Junsun Park / Hyunmin Kim / Daniel Gestaut / Seyeon Lim / Kwadwo A Opoku-Nsiah / Alexander Leitner / Judith Frydman / Soung-Hun Roh / 要旨: Proper cellular proteostasis, essential for viability, requires a network of chaperones and cochaperones. ATP-dependent chaperonin TRiC/CCT partners with cochaperones prefoldin (PFD) and phosducin- ...Proper cellular proteostasis, essential for viability, requires a network of chaperones and cochaperones. ATP-dependent chaperonin TRiC/CCT partners with cochaperones prefoldin (PFD) and phosducin-like proteins (PhLPs) to facilitate folding of essential eukaryotic proteins. Using cryoEM and biochemical analyses, we determine the ATP-driven cycle of TRiC-PFD-PhLP2A interaction. PhLP2A binds to open apo-TRiC through polyvalent domain-specific contacts with its chamber's equatorial and apical regions. PhLP2A N-terminal H3-domain binding to subunits CCT3/4 apical domains displace PFD from TRiC. ATP-induced TRiC closure rearranges the contacts of PhLP2A domains within the closed chamber. In the presence of substrate, actin and PhLP2A segregate into opposing chambers, each binding to positively charged inner surface residues from CCT1/3/6/8. Notably, actin induces a conformational change in PhLP2A, causing its N-terminal helices to extend across the inter-ring interface to directly contact a hydrophobic groove in actin. Our findings reveal an ATP-driven PhLP2A structural rearrangement cycle within the TRiC chamber to facilitate folding. | |||||||||
履歴 |
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-構造の表示
添付画像 |
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-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_35122.map.gz | 118.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-35122-v30.xml emd-35122.xml | 40.3 KB 40.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_35122_fsc.xml | 10.5 KB | 表示 | FSCデータファイル |
画像 | emd_35122.png | 81.1 KB | ||
Filedesc metadata | emd-35122.cif.gz | 10.1 KB | ||
その他 | emd_35122_additional_1.map.gz emd_35122_additional_2.map.gz emd_35122_additional_3.map.gz emd_35122_half_map_1.map.gz emd_35122_half_map_2.map.gz | 96.5 MB 96.3 MB 117.9 MB 116.2 MB 116.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-35122 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35122 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_35122_validation.pdf.gz | 1.3 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_35122_full_validation.pdf.gz | 1.3 MB | 表示 | |
XML形式データ | emd_35122_validation.xml.gz | 19.5 KB | 表示 | |
CIF形式データ | emd_35122_validation.cif.gz | 24.9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35122 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35122 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_35122.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | A primary EM map | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: Additional map of TRiC with truncated PhLP2A mutant(TXD-CTD)...
ファイル | emd_35122_additional_1.map | ||||||||||||
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注釈 | Additional map of TRiC with truncated PhLP2A mutant(TXD-CTD) in the closed state | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Additional map of TRiC with truncated PhLP2A mutant(NTD-TXD)...
ファイル | emd_35122_additional_2.map | ||||||||||||
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注釈 | Additional map of TRiC with truncated PhLP2A mutant(NTD-TXD) in the closed state | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Additional map of TRiC with truncated PhLP2A mutant(TXD)...
ファイル | emd_35122_additional_3.map | ||||||||||||
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注釈 | Additional map of TRiC with truncated PhLP2A mutant(TXD) in the closed state | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: An EM half map
ファイル | emd_35122_half_map_1.map | ||||||||||||
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注釈 | An EM half map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: An EM half map
ファイル | emd_35122_half_map_2.map | ||||||||||||
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注釈 | An EM half map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Complex of TRiC/CCT-PhLP2A treated with ATP-AlFx
+超分子 #1: Complex of TRiC/CCT-PhLP2A treated with ATP-AlFx
+超分子 #2: Human TRiC/CCT complex
+超分子 #3: PhLP2A (PDCL3)
+分子 #1: T-complex protein 1 subunit alpha
+分子 #2: T-complex protein 1 subunit beta
+分子 #3: T-complex protein 1 subunit gamma
+分子 #4: T-complex protein 1 subunit delta
+分子 #5: T-complex protein 1 subunit epsilon
+分子 #6: T-complex protein 1 subunit zeta
+分子 #7: T-complex protein 1 subunit eta
+分子 #8: T-complex protein 1 subunit theta
+分子 #9: Phosducin-like protein 3
+分子 #10: ADENOSINE-5'-DIPHOSPHATE
+分子 #11: MAGNESIUM ION
+分子 #12: ALUMINUM FLUORIDE
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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解析 | 単粒子再構成法 |
試料の集合状態 | 2D array |
-試料調製
緩衝液 | pH: 7.4 構成要素:
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グリッド | モデル: Quantifoil R1.2/1.3 / 材質: COPPER / メッシュ: 200 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY | |||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK IV |
-電子顕微鏡法
顕微鏡 | FEI TALOS ARCTICA |
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撮影 | フィルム・検出器のモデル: FEI FALCON IV (4k x 4k) 検出モード: COUNTING / デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / 実像数: 1368 / 平均電子線量: 40.0 e/Å2 |
電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 1.0 µm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Talos Arctica / 画像提供: FEI Company |