+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2348 | |||||||||
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タイトル | Structure of the 26S proteasome with ATP-yS bound provides insights into the mechanism of nucleotide-dependent substrate translocation | |||||||||
マップデータ | Reconstruction of 26S Proteasome in ATP-yS | |||||||||
試料 |
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キーワード | Proteasome (プロテアソーム) / AAA-ATPase / ATP-analog | |||||||||
機能・相同性 | 機能・相同性情報 SAGA complex localization to transcription regulatory region / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / nonfunctional rRNA decay / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome ...SAGA complex localization to transcription regulatory region / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / nonfunctional rRNA decay / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / protein-containing complex localization / mitochondrial fission / proteasome regulatory particle, base subcomplex / K48-linked polyubiquitin modification-dependent protein binding / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / Ub-specific processing proteases / peptide catabolic process / proteasome binding / regulation of protein catabolic process / protein deubiquitination / proteasome storage granule / polyubiquitin modification-dependent protein binding / endopeptidase activator activity / proteasome assembly / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / enzyme regulator activity / mRNA export from nucleus / : / protein folding chaperone / Neutrophil degranulation / proteasome complex / ubiquitin binding / proteasomal protein catabolic process / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / positive regulation of protein catabolic process / metallopeptidase activity / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / regulation of cell cycle / クロマチンリモデリング / protein domain specific binding / mRNA binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / structural molecule activity / 小胞体 / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / ミトコンドリア / ATP binding / identical protein binding / metal ion binding / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 9.8 Å | |||||||||
データ登録者 | Sledz P / Unverdorben P / Beck F / Pfeifer G / Schweitzer A / Foerster F / Baumeister W | |||||||||
引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2013 タイトル: Structure of the 26S proteasome with ATP-γS bound provides insights into the mechanism of nucleotide-dependent substrate translocation. 著者: Paweł Śledź / Pia Unverdorben / Florian Beck / Günter Pfeifer / Andreas Schweitzer / Friedrich Förster / Wolfgang Baumeister / 要旨: The 26S proteasome is a 2.5-MDa, ATP-dependent multisubunit proteolytic complex that processively destroys proteins carrying a degradation signal. The proteasomal ATPase heterohexamer is a key module ...The 26S proteasome is a 2.5-MDa, ATP-dependent multisubunit proteolytic complex that processively destroys proteins carrying a degradation signal. The proteasomal ATPase heterohexamer is a key module of the 19S regulatory particle; it unfolds substrates and translocates them into the 20S core particle where degradation takes place. We used cryoelectron microscopy single-particle analysis to obtain insights into the structural changes of 26S proteasome upon the binding and hydrolysis of ATP. The ATPase ring adopts at least two distinct helical staircase conformations dependent on the nucleotide state. The transition from the conformation observed in the presence of ATP to the predominant conformation in the presence of ATP-γS induces a sliding motion of the ATPase ring over the 20S core particle ring leading to an alignment of the translocation channels of the ATPase and the core particle gate, a conformational state likely to facilitate substrate translocation. Two types of intersubunit modules formed by the large ATPase domain of one ATPase subunit and the small ATPase domain of its neighbor exist. They resemble the contacts observed in the crystal structures of ClpX and proteasome-activating nucleotidase, respectively. The ClpX-like contacts are positioned consecutively and give rise to helical shape in the hexamer, whereas the proteasome-activating nucleotidase-like contact is required to close the ring. Conformational switching between these forms allows adopting different helical conformations in different nucleotide states. We postulate that ATP hydrolysis by the regulatory particle ATPase (Rpt) 5 subunit initiates a cascade of conformational changes, leading to pulling of the substrate, which is primarily executed by Rpt1, Rpt2, and Rpt6. | |||||||||
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_2348.map.gz | 78.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-2348-v30.xml emd-2348.xml | 8.6 KB 8.6 KB | 表示 表示 | EMDBヘッダ |
画像 | 2348-imgMap.jpg | 28.2 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2348 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2348 | 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_2348.map.gz / 形式: CCP4 / 大きさ: 81.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of 26S Proteasome in ATP-yS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.99 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 : 26S Proteasome from Saccharomyces cerevisiae
全体 | 名称: 26S Proteasome from Saccharomyces cerevisiaeプロテアソーム |
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要素 |
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-超分子 #1000: 26S Proteasome from Saccharomyces cerevisiae
超分子 | 名称: 26S Proteasome from Saccharomyces cerevisiae / タイプ: sample / ID: 1000 / Number unique components: 1 |
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分子量 | 実験値: 2.5 MDa / 理論値: 2.5 MDa |
-分子 #1: 26S Proteasome
分子 | 名称: 26S Proteasome / タイプ: protein_or_peptide / ID: 1 / 組換発現: No |
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由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) / 別称: baker's yeast |
分子量 | 実験値: 2.5 MDa / 理論値: 2.5 MDa |
-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 | particle |
-試料調製
濃度 | 0.3 mg/mL |
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緩衝液 | pH: 7.4 / 詳細: 1 mM ATP-yS, 40 mM NaCL, 20MM HEPES, 10mM MgCl2 |
凍結 | 凍結剤: ETHANE / 装置: HOMEMADE PLUNGER / 手法: Blot for 2 seconds before plunging |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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電子線 | 加速電圧: 200 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 151456 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELDBright-field microscopy / Cs: 2 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): 1.0 µm / 倍率(公称値): 47000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
日付 | 2012年2月28日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: TVIPS TEMCAM-F816 (8k x 8k) 実像数: 10000 / 平均電子線量: 20 e/Å2 / ビット/ピクセル: 14 |
Tilt angle min | 0 |
Tilt angle max | 0 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | 詳細: micrograph |
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最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 9.8 Å / 解像度の算出法: FSC 0.5 CUT-OFF / ソフトウェア - 名称: xmipp / 使用した粒子像数: 280000 |