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基本情報
登録情報 | データベース: EMDB / ID: EMD-2937 | |||||||||
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タイトル | Electron cryo-microscopy structure of PB1-p62 type T filaments | |||||||||
![]() | 3D reconstruction of PB1(1-122) type T | |||||||||
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![]() | Selective autophagy / autophagy receptor / autophagy scaffold / p62/SQSTM1 / single-particle helical reconstruction | |||||||||
機能・相同性 | ![]() brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein binding / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to stress / response to mitochondrial depolarisation / positive regulation of mitophagy in response to mitochondrial depolarization / aggrephagy ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / protein binding / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to stress / response to mitochondrial depolarisation / positive regulation of mitophagy in response to mitochondrial depolarization / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / regulation of autophagy of mitochondrion / pexophagy / regulation of protein complex stability / protein heterooligomerization / autophagy of mitochondrion / endosome organization / non-membrane-bounded organelle assembly / molecular sequestering activity / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / ubiquitin-modified protein reader activity / Nuclear events mediated by NFE2L2 / autolysosome / K63-linked polyubiquitin modification-dependent protein binding / intracellular non-membrane-bounded organelle / endosomal transport / temperature homeostasis / immune system process / neurotrophin TRK receptor signaling pathway / mitophagy / positive regulation of macroautophagy / autophagosome / positive regulation of autophagy / energy homeostasis / signaling adaptor activity / inclusion body / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / Pexophagy / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / sarcomere / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / macroautophagy / apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / protein kinase C binding / ionotropic glutamate receptor binding / P-body / protein catabolic process / protein localization / receptor tyrosine kinase binding / PML body / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / Signaling by ALK fusions and activated point mutants / late endosome / protein-macromolecule adaptor activity / Neddylation / signaling receptor activity / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / cell differentiation / lysosome / intracellular signal transduction / endosome / positive regulation of protein phosphorylation / positive regulation of apoptotic process / protein phosphorylation / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / negative regulation of apoptotic process / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / extracellular exosome / nucleoplasm / identical protein binding 類似検索 - 分子機能 | |||||||||
生物種 | ![]() | |||||||||
手法 | らせん対称体再構成法 / クライオ電子顕微鏡法 / 解像度: 10.3 Å | |||||||||
![]() | Ciuffa R / Lamark T / Tarafder A / Guesdon A / Rybina S / Hagen WJH / Johansen T / Sachse C | |||||||||
![]() | ![]() タイトル: The selective autophagy receptor p62 forms a flexible filamentous helical scaffold. 著者: Rodolfo Ciuffa / Trond Lamark / Abul K Tarafder / Audrey Guesdon / Sofia Rybina / Wim J H Hagen / Terje Johansen / Carsten Sachse / ![]() ![]() 要旨: The scaffold protein p62/SQSTM1 is involved in protein turnover and signaling and is commonly found in dense protein bodies in eukaryotic cells. In autophagy, p62 acts as a selective autophagy ...The scaffold protein p62/SQSTM1 is involved in protein turnover and signaling and is commonly found in dense protein bodies in eukaryotic cells. In autophagy, p62 acts as a selective autophagy receptor that recognizes and shuttles ubiquitinated proteins to the autophagosome for degradation. The structural organization of p62 in cellular bodies and the interplay of these assemblies with ubiquitin and the autophagic marker LC3 remain to be elucidated. Here, we present a cryo-EM structural analysis of p62. Together with structures of assemblies from the PB1 domain, we show that p62 is organized in flexible polymers with the PB1 domain constituting a helical scaffold. Filamentous p62 is capable of binding LC3 and addition of long ubiquitin chains induces disassembly and shortening of filaments. These studies explain how p62 assemblies provide a large molecular scaffold for the nascent autophagosome and reveal how they can bind ubiquitinated cargo. | |||||||||
履歴 |
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構造の表示
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構造ビューア | EMマップ: ![]() ![]() ![]() |
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マップデータ | ![]() | 12.2 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 23.3 KB 23.3 KB | 表示 表示 | ![]() |
画像 | ![]() | 443 KB | ||
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-検証レポート
文書・要旨 | ![]() | 213.4 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 212.5 KB | 表示 | |
XML形式データ | ![]() | 4.6 KB | 表示 | |
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 | 3D reconstruction of PB1(1-122) type T | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.372 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 : PB1(1-122) domain of p62/Sqstm1
全体 | 名称: PB1(1-122) domain of p62/Sqstm1 |
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要素 |
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-超分子 #1000: PB1(1-122) domain of p62/Sqstm1
超分子 | 名称: PB1(1-122) domain of p62/Sqstm1 / タイプ: sample / ID: 1000 / 詳細: Helical polymer / 集合状態: Helical / Number unique components: 1 |
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分子量 | 実験値: 13.7 KDa / 理論値: 13.7 KDa / 手法: Theoretical weight of construct |
-分子 #1: Sequestosome-1
分子 | 名称: Sequestosome-1 / タイプ: protein_or_peptide / ID: 1 / Name.synonym: p62/SQSTM1 / 集合状態: Helical / 組換発現: Yes |
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由来(天然) | 生物種: ![]() |
分子量 | 実験値: 13.7 KDa / 理論値: 13.7 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | UniProtKB: Sequestosome-1 GO: phagophore assembly site, autophagy of mitochondrion, P-body, P-body, positive regulation of protein phosphorylation, immune system process, protein serine/threonine kinase activity, protein ...GO: phagophore assembly site, autophagy of mitochondrion, P-body, P-body, positive regulation of protein phosphorylation, immune system process, protein serine/threonine kinase activity, protein kinase C binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, protein binding, nucleus, nucleus, nucleoplasm, cytoplasm, cytoplasm, cytoplasm, lysosome, lysosome, endosome, late endosome, autophagosome, autophagosome, autophagosome, endoplasmic reticulum, endoplasmic reticulum, cytosol, cytosol, cytosol, cytosol, cytosol, cytosol, cytosol, cytosol, cytosol, cytosol, protein phosphorylation, ubiquitin-dependent protein catabolic process, autophagy, autophagy, autophagy, apoptotic process, response to stress, protein localization, zinc ion binding, regulation of mitochondrion organization, endosomal transport, inclusion body, aggresome, aggresome, macroautophagy, positive regulation of macroautophagy, PML body, protein kinase binding, cell differentiation, receptor tyrosine kinase binding, cytoplasmic vesicle, intracellular signal transduction, SH2 domain binding, identical protein binding, identical protein binding, identical protein binding, identical protein binding, identical protein binding, protein homodimerization activity, positive regulation of apoptotic process, negative regulation of apoptotic process, regulation of canonical NF-kappaB signal transduction, ubiquitin binding, positive regulation of transcription by RNA polymerase II, regulation of Ras protein signal transduction, metal ion binding, neurotrophin TRK receptor signaling pathway, neurotrophin TRK receptor signaling pathway, protein heterooligomerization, extracellular exosome, K63-linked polyubiquitin modification-dependent protein binding, apoptotic signaling pathway, positive regulation of mitophagy in response to mitochondrial depolarization, regulation of autophagy of mitochondrion InterPro: PB1 domain, UBA-like superfamily, Ubiquitin-associated domain, Zinc finger, ZZ-type |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | らせん対称体再構成法 |
試料の集合状態 | helical array |
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試料調製
濃度 | 0.25 mg/mL |
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緩衝液 | pH: 7.5 / 詳細: 50 mM Tris pH 7.5, 100 mM NaCl, DTT 4 mM |
グリッド | 詳細: glow-discharged C-flat 1.2/1.3 and 200 mesh Quantifoil multi-A grids |
凍結 | 凍結剤: ETHANE / チャンバー内温度: 77 K / 装置: HOMEMADE PLUNGER / 手法: Backside blotting |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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日付 | 2012年10月9日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) 実像数: 443 / 平均電子線量: 10 e/Å2 |
電子線 | 加速電圧: 120 kV / 電子線源: ![]() |
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): 3.5 µm / 最小 デフォーカス(公称値): 1.5 µm / 倍率(公称値): 59000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
詳細 | All of the image processing was carried using the SPRING package. |
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最終 再構成 | 想定した対称性 - らせんパラメータ - Δz: 10.09 Å 想定した対称性 - らせんパラメータ - ΔΦ: 26.71 ° 想定した対称性 - らせんパラメータ - 軸対称性: C1 (非対称) アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 10.3 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: SPRING |
CTF補正 | 詳細: CTFFIND, convolution images, Wiener filter reconstruction |
最終 角度割当 | 詳細: SPIDER |