+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2936 | |||||||||
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タイトル | Electron cryo-microscopy structure of PB1-p62 filaments | |||||||||
マップデータ | 3D reconstruction of PB1(1-102) p62 | |||||||||
試料 |
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キーワード | Selective autophagy / autophagy receptor / autophagy scaffold / p62/SQSTM1 / single-particle helical reconstruction | |||||||||
機能・相同性 | 機能・相同性情報 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 mitochondrial depolarisation / aggrephagy / amphisome / positive regulation of mitophagy in response to mitochondrial depolarization ...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 mitochondrial depolarisation / aggrephagy / amphisome / positive regulation of mitophagy in response to mitochondrial depolarization / negative regulation of toll-like receptor 4 signaling pathway / regulation of autophagy of mitochondrion / autophagy of mitochondrion / pexophagy / protein heterooligomerization / regulation of protein complex stability / endosome organization / response to stress / non-membrane-bounded organelle assembly / molecular sequestering activity / ubiquitin-modified protein reader activity / phagophore assembly site / regulation of mitochondrion organization / aggresome / regulation of canonical NF-kappaB signal transduction / Nuclear events mediated by NFE2L2 / negative regulation of ferroptosis / autolysosome / endosomal transport / intracellular non-membrane-bounded organelle / temperature homeostasis / immune system process / K63-linked polyubiquitin modification-dependent protein binding / neurotrophin TRK receptor signaling pathway / positive regulation of macroautophagy / mitophagy / autophagosome / positive regulation of autophagy / signaling adaptor activity / energy homeostasis / inclusion body / sperm midpiece / negative regulation of protein ubiquitination / protein sequestering activity / ionotropic glutamate receptor binding / p75NTR recruits signalling complexes / PINK1-PRKN Mediated Mitophagy / Pexophagy / sarcomere / positive regulation of protein localization to plasma membrane / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / SH2 domain binding / molecular condensate scaffold activity / ubiquitin binding / positive regulation of long-term synaptic potentiation / response to ischemia / macroautophagy / apoptotic signaling pathway / protein kinase C binding / P-body / protein catabolic process / PML body / receptor tyrosine kinase binding / autophagy / Interleukin-1 signaling / protein import into nucleus / KEAP1-NFE2L2 pathway / protein localization / Signaling by ALK fusions and activated point mutants / late endosome / signaling receptor activity / Neddylation / protein-macromolecule adaptor activity / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / endosome / cell differentiation / lysosome / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / protein phosphorylation / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein-containing complex binding / protein kinase binding / apoptotic process / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / mitochondrion / zinc ion binding / extracellular exosome / nucleoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
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: 10.9 Å | |||||||||
データ登録者 | Ciuffa R / Lamark T / Tarafder A / Guesdon A / Rybina S / Hagen WJH / Johansen T / Sachse C | |||||||||
引用 | ジャーナル: Cell Rep / 年: 2015 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
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_2936.map.gz | 2.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-2936-v30.xml emd-2936.xml | 23.3 KB 23.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_2936.png | 438.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2936 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2936 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_2936_validation.pdf.gz | 213.3 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_2936_full_validation.pdf.gz | 212.5 KB | 表示 | |
XML形式データ | emd_2936_validation.xml.gz | 4.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2936 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2936 | 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_2936.map.gz / 形式: CCP4 / 大きさ: 4.5 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | 3D reconstruction of PB1(1-102) p62 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.16 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
-試料の構成要素
-全体 : PB1(1-102) domain of p62/Sqstm1
全体 | 名称: PB1(1-102) domain of p62/Sqstm1 |
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要素 |
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-超分子 #1000: PB1(1-102) domain of p62/Sqstm1
超分子 | 名称: PB1(1-102) 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: 11.3 KDa / 理論値: 11.3 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: Homo sapiens (ヒト) / 別称: Human |
分子量 | 実験値: 11.3 KDa / 理論値: 11.3 KDa |
組換発現 | 生物種: Escherichia coli (大腸菌) / 組換株: BL21 / 組換プラスミド: pOPTM-p62-PB1_K103STOP_E104STOP |
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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解析 | らせん対称体再構成法 |
試料の集合状態 | helical array |
-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 |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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日付 | 2014年2月21日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 実像数: 994 / 平均電子線量: 15 e/Å2 |
電子線 | 加速電圧: 300 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): 5.0 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 75000 |
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 |
-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: 12.99 Å 想定した対称性 - らせんパラメータ - ΔΦ: 30.77 ° 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: 10.9 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 |