+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2165 | |||||||||
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タイトル | Cryo-EM reconstruction of the yeast 26S proteasome | |||||||||
マップデータ | Reconstruction of Saccharomyces cerevisiase 26S proteasome | |||||||||
試料 |
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キーワード | 26S proteasome / AAA-ATPases / protein degradation / ubiquitin-proteasome pathway | |||||||||
機能・相同性 | 機能・相同性情報 SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / 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 ...SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / 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 / protein-containing complex localization / proteasome-activating activity / mitochondrial fission / metal-dependent deubiquitinase activity / 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 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / proteasome binding / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / peptide catabolic process / regulation of protein catabolic process / Orc1 removal from chromatin / protein deubiquitination / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / polyubiquitin modification-dependent protein binding / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / Ub-specific processing proteases / positive regulation of RNA polymerase II transcription preinitiation complex assembly / mRNA export from nucleus / enzyme regulator activity / ERAD pathway / protein folding chaperone / Neutrophil degranulation / proteasome complex / ubiquitin binding / 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 / chromatin remodeling / protein domain specific binding / mRNA binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / mitochondrion / ATP binding / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol 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: 7.4 Å | |||||||||
データ登録者 | Beck F / Unverdorben P / Bohn S / Schweitzer A / Pfeifer G / Sakata E / Nickell S / Plitzko JM / Villa E / Baumeister W / Forster F | |||||||||
引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2012 タイトル: Near-atomic resolution structural model of the yeast 26S proteasome. 著者: Florian Beck / Pia Unverdorben / Stefan Bohn / Andreas Schweitzer / Günter Pfeifer / Eri Sakata / Stephan Nickell / Jürgen M Plitzko / Elizabeth Villa / Wolfgang Baumeister / Friedrich Förster / 要旨: The 26S proteasome operates at the executive end of the ubiquitin-proteasome pathway. Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a resolution of 7.4 Å or ...The 26S proteasome operates at the executive end of the ubiquitin-proteasome pathway. Here, we present a cryo-EM structure of the Saccharomyces cerevisiae 26S proteasome at a resolution of 7.4 Å or 6.7 Å (Fourier-Shell Correlation of 0.5 or 0.3, respectively). We used this map in conjunction with molecular dynamics-based flexible fitting to build a near-atomic resolution model of the holocomplex. The quality of the map allowed us to assign α-helices, the predominant secondary structure element of the regulatory particle subunits, throughout the entire map. We were able to determine the architecture of the Rpn8/Rpn11 heterodimer, which had hitherto remained elusive. The MPN domain of Rpn11 is positioned directly above the AAA-ATPase N-ring suggesting that Rpn11 deubiquitylates substrates immediately following commitment and prior to their unfolding by the AAA-ATPase module. The MPN domain of Rpn11 dimerizes with that of Rpn8 and the C-termini of both subunits form long helices, which are integral parts of a coiled-coil module. Together with the C-terminal helices of the six PCI-domain subunits they form a very large coiled-coil bundle, which appears to serve as a flexible anchoring device for all the lid subunits. | |||||||||
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_2165.map.gz | 78.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-2165-v30.xml emd-2165.xml | 9.1 KB 9.1 KB | 表示 表示 | EMDBヘッダ |
画像 | 2165_26S_cerevisiae.tif | 160.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2165 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2165 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_2165_validation.pdf.gz | 309.9 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_2165_full_validation.pdf.gz | 309.5 KB | 表示 | |
XML形式データ | emd_2165_validation.xml.gz | 6.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2165 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2165 | 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_2165.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 Saccharomyces cerevisiase 26S proteasome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : Saccharomyes cerevisiae 26S proteasome
全体 | 名称: Saccharomyes cerevisiae 26S proteasome |
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要素 |
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-超分子 #1000: Saccharomyes cerevisiae 26S proteasome
超分子 | 名称: Saccharomyes cerevisiae 26S proteasome / 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 |
-超分子 #1: 26S proteasome
超分子 | 名称: 26S proteasome / タイプ: organelle_or_cellular_component / 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 | 0.5 mg/mL |
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緩衝液 | pH: 7.1 詳細: 4 mM ATP, 10mM MgCl2, 50mM Tris[pH7.1], 10% glycerol |
グリッド | 詳細: quantifoil holey carbon |
凍結 | 凍結剤: ETHANE / 装置: HOMEMADE PLUNGER |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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温度 | 最低: 80 K / 最高: 81 K / 平均: 80.5 K |
日付 | 2012年3月15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: 63126 / 平均電子線量: 25 e/Å2 / ビット/ピクセル: 16 |
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): 156784 / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 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): 1.5 µm / 倍率(公称値): 150000 |
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 | The particles were selected using an automatic selection program. |
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CTF補正 | 詳細: micrograph |
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: 7.4 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: 2464694 |