+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-2590 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Inter-ring rotations of AAA ATPase p97 | |||||||||
マップデータ | Reconstruction of p97 in presence of ADP, conformation 1 | |||||||||
試料 |
| |||||||||
キーワード | AAA ATPase / p97 | |||||||||
機能・相同性 | 機能・相同性情報 RHOH GTPase cycle / HSF1 activation / Translesion Synthesis by POLH / Protein methylation / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / KEAP1-NFE2L2 pathway / ABC-family proteins mediated transport ...RHOH GTPase cycle / HSF1 activation / Translesion Synthesis by POLH / Protein methylation / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Ovarian tumor domain proteases / Hedgehog ligand biogenesis / KEAP1-NFE2L2 pathway / ABC-family proteins mediated transport / Neddylation / positive regulation of ubiquitin-dependent protein catabolic process / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / protein-DNA covalent cross-linking repair / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / aggresome assembly / vesicle-fusing ATPase / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / retrograde protein transport, ER to cytosol / K48-linked polyubiquitin modification-dependent protein binding / regulation of synapse organization / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / ATPase complex / MHC class I protein binding / polyubiquitin modification-dependent protein binding / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / proteasomal protein catabolic process / translesion synthesis / interstrand cross-link repair / ERAD pathway / negative regulation of smoothened signaling pathway / ATP metabolic process / Neutrophil degranulation / proteasome complex / viral genome replication / lipid droplet / macroautophagy / positive regulation of protein-containing complex assembly / ADP binding / autophagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of canonical Wnt signaling pathway / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / myelin sheath / site of double-strand break / cellular response to heat / ubiquitin-dependent protein catabolic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protein ubiquitination / protein domain specific binding / DNA repair / lipid binding / glutamatergic synapse / ubiquitin protein ligase binding / DNA damage response / synapse / endoplasmic reticulum membrane / protein-containing complex binding / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Mus musculus (ハツカネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 20.0 Å | |||||||||
データ登録者 | Yeung HO / Forster A / Bebeacua C / Niwa H / Ewens C / McKeown C / Zhang X / Freemont PS | |||||||||
引用 | ジャーナル: Open Biol / 年: 2014 タイトル: Inter-ring rotations of AAA ATPase p97 revealed by electron cryomicroscopy. 著者: Heidi O Yeung / Andreas Förster / Cecilia Bebeacua / Hajime Niwa / Caroline Ewens / Ciarán McKeown / Xiaodong Zhang / Paul S Freemont / 要旨: The type II AAA+ protein p97 is involved in numerous cellular activities, including endoplasmic reticulum-associated degradation, transcription activation, membrane fusion and cell-cycle control. ...The type II AAA+ protein p97 is involved in numerous cellular activities, including endoplasmic reticulum-associated degradation, transcription activation, membrane fusion and cell-cycle control. These activities are at least in part regulated by the ubiquitin system, in which p97 is thought to target ubiquitylated protein substrates within macromolecular complexes and assist in their extraction or disassembly. Although ATPase activity is essential for p97 function, little is known about how ATP binding or hydrolysis is coupled with p97 conformational changes and substrate remodelling. Here, we have used single-particle electron cryomicroscopy (cryo-EM) to study the effect of nucleotides on p97 conformation. We have identified conformational heterogeneity within the cryo-EM datasets from which we have resolved two major p97 conformations. A comparison of conformations reveals inter-ring rotations upon nucleotide binding and hydrolysis that may be linked to the remodelling of target protein complexes. | |||||||||
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 | 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_2590.map.gz | 365.3 KB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-2590-v30.xml emd-2590.xml | 9.9 KB 9.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_2590.jpg | 49.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-2590 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2590 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_2590_validation.pdf.gz | 190.7 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_2590_full_validation.pdf.gz | 189.9 KB | 表示 | |
XML形式データ | emd_2590_validation.xml.gz | 5.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2590 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2590 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_2590.map.gz / 形式: CCP4 / 大きさ: 3.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Reconstruction of p97 in presence of ADP, conformation 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 3.53 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-試料の構成要素
-全体 : p97 in presence of ADP, conformation 1
全体 | 名称: p97 in presence of ADP, conformation 1 |
---|---|
要素 |
|
-超分子 #1000: p97 in presence of ADP, conformation 1
超分子 | 名称: p97 in presence of ADP, conformation 1 / タイプ: sample / ID: 1000 / 詳細: p97 E578Q mutant comprising residues 22-806 / 集合状態: homohexamer / Number unique components: 1 |
---|---|
分子量 | 理論値: 550 KDa |
-分子 #1: Transitional endoplasmic reticulum ATPase
分子 | 名称: Transitional endoplasmic reticulum ATPase / タイプ: protein_or_peptide / ID: 1 / Name.synonym: VCP, P97 / コピー数: 6 / 集合状態: Hexamer / 組換発現: Yes |
---|---|
由来(天然) | 生物種: Mus musculus (ハツカネズミ) / 別称: House mouse |
分子量 | 理論値: 90 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) / 組換プラスミド: pET28 |
配列 | UniProtKB: Transitional endoplasmic reticulum ATPase |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
濃度 | 2.8 mg/mL |
---|---|
緩衝液 | pH: 8 / 詳細: 250 mM NaCl, 25 mM Tris, 2.5 mM MgCl2 |
グリッド | 詳細: carbon film on copper grids |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK II / 手法: Blot for two seconds before plunging. |
-電子顕微鏡法
顕微鏡 | FEI/PHILIPS CM200FEG |
---|---|
日付 | 2008年5月10日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: TVIPS TEMCAM-F415 (4k x 4k) |
電子線 | 加速電圧: 200 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: 2.1 mm |
試料ステージ | 試料ホルダーモデル: GATAN HELIUM |
-画像解析
最終 再構成 | 想定した対称性 - 点群: C6 (6回回転対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 20.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: Imagic / 使用した粒子像数: 30300 |
---|---|
最終 2次元分類 | クラス数: 2 |
-原子モデル構築 1
初期モデル | PDB ID: Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C |
---|---|
ソフトウェア | 名称: VEDA |
詳細 | N, D1 and D2 domains fitted separately under imposition of sixfold symmetry |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: correlation coefficient |
-原子モデル構築 2
初期モデル | PDB ID: Chain - Chain ID: A |
---|---|
ソフトウェア | 名称: VEDA |
詳細 | N, D1 and D2 domains fitted separately under imposition of sixfold symmetry |
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT / 当てはまり具合の基準: correlation coefficient |