+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4uf8 | ||||||
---|---|---|---|---|---|---|---|
タイトル | Electron cryo-microscopy structure of PB1-p62 filaments | ||||||
要素 | SEQUESTOSOME-1 | ||||||
キーワード | SIGNALING PROTEIN / 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 / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / pexophagy ...brown fat cell proliferation / protein localization to perinuclear region of cytoplasm / regulation of Ras protein signal transduction / protein targeting to vacuole involved in autophagy / Lewy body / response to mitochondrial depolarisation / aggrephagy / amphisome / negative regulation of toll-like receptor 4 signaling pathway / pexophagy / regulation of protein complex stability / 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 / mitophagy / 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 / protein kinase C binding / positive regulation of protein localization to plasma membrane / 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 / ubiquitin-dependent protein catabolic process / transcription by RNA polymerase II / cell differentiation / intracellular signal transduction / positive regulation of protein phosphorylation / positive regulation of apoptotic process / intracellular membrane-bounded organelle / apoptotic process / ubiquitin protein ligase binding / protein-containing complex binding / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / extracellular exosome / nucleoplasm / identical protein 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 / 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, W.J.H. / 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 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
構造ビューア | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 4uf8.cif.gz | 76.3 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb4uf8.ent.gz | 59.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 4uf8.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 | 4uf8_validation.pdf.gz | 738 KB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 4uf8_full_validation.pdf.gz | 743.7 KB | 表示 | |
XML形式データ | 4uf8_validation.xml.gz | 15.6 KB | 表示 | |
CIF形式データ | 4uf8_validation.cif.gz | 21.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/uf/4uf8 ftp://data.pdbj.org/pub/pdb/validation_reports/uf/4uf8 | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
| x 20
2 |
|
3 |
|
対称性 | らせん対称: (回転対称性: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 20 / Rise per n subunits: 12.99 Å / Rotation per n subunits: -30.77 °) |
-要素
#1: タンパク質 | 分子量: 11120.575 Da / 分子数: 4 / 断片: PB1 DOMAIN, RESIDUES 3-102 / 由来タイプ: 組換発現 / 由来: (組換発現) HOMO SAPIENS (ヒト) / プラスミド: POPTM-P62-PB1_K103STOP_E104STOP / 発現宿主: ESCHERICHIA COLI (大腸菌) / 株 (発現宿主): BL21 / 参照: UniProt: Q13501 |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
EM実験 | 試料の集合状態: FILAMENT / 3次元再構成法: らせん対称体再構成法 |
-試料調製
構成要素 | 名称: PB1(1-102) DOMAIN OF P62 SQSTM1 / タイプ: COMPLEX |
---|---|
緩衝液 | 名称: 50 MM TRIS PH 7.5, 100 MM NACL, DTT 4 MM / pH: 7.5 / 詳細: 50 MM TRIS PH 7.5, 100 MM NACL, DTT 4 MM |
試料 | 濃度: 0.25 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: HOLEY CARBON |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE 詳細: VITRIFICATION 1 -- CRYOGEN- ETHANE, TEMPERATURE- 77, INSTRUMENT- HOMEMADE PLUNGER METHOD- BACKSIDE BLOTTING, |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
---|---|
顕微鏡 | モデル: FEI TITAN KRIOS / 日付: 2014年2月21日 |
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 / 倍率(公称値): 75000 X / 最大 デフォーカス(公称値): 5000 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm |
撮影 | 電子線照射量: 15 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
画像スキャン | デジタル画像の数: 994 |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | 詳細: CTFFIND, CONVOLUTION IMAGES WIENER FILTER RECONSTRUCTION | ||||||||||||
3次元再構成 | 手法: PROJECTION MATCHING / 解像度: 10.9 Å / 粒子像の数: 50620 / ピクセルサイズ(公称値): 2.16 Å / ピクセルサイズ(実測値): 2.16 Å 詳細: SINGLE-PARTICLE BASED HELICAL RECONSTRUCTION USING SPRING. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2936. (DEPOSITION ID: 13197) 対称性のタイプ: HELICAL | ||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL / 詳細: METHOD--RIGID BODY REFINEMENT PROTOCOL--NMR | ||||||||||||
原子モデル構築 | PDB-ID: 2KKC Accession code: 2KKC / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化 | 最高解像度: 10.9 Å | ||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 10.9 Å
|