+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-3298 | |||||||||
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タイトル | Cryo-EM structure of human p97 bound to ATPgS (Conformation II) | |||||||||
マップデータ | Reconstruction of human p97 bound to ATPgS (conformation II). | |||||||||
試料 |
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キーワード | cryo-electron microscopy / single-particle / p97 / AAA ATPase | |||||||||
機能・相同性 | 機能・相同性情報 protein binding / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / cytoplasm protein quality control / 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 ...protein binding / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / cytoplasm protein quality control / 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 aerobic respiration / regulation of synapse organization / positive regulation of ATP biosynthetic process / ubiquitin-specific protease binding / ATPase complex / MHC class I protein binding / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / HSF1 activation / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / proteasomal protein catabolic process / translesion synthesis / Protein methylation / interstrand cross-link repair / ATP metabolic process / negative regulation of smoothened signaling pathway / ERAD pathway / endoplasmic reticulum unfolded protein response / Attachment and Entry / proteasome complex / viral genome replication / lipid droplet / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / macroautophagy / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / positive regulation of protein-containing complex assembly / ADP binding / Translesion Synthesis by POLH / establishment of protein localization / ABC-family proteins mediated transport / : / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / positive regulation of canonical Wnt signaling pathway / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / Neddylation / cellular response to heat / ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / signaling receptor binding / DNA repair / lipid binding / glutamatergic synapse / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / unidentified (未定義) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.2 Å | |||||||||
データ登録者 | Banerjee S / Bartesaghi A / Merk A / Rao P / Bulfer SL / Yan Y / Green N / Mroczkowski B / Neitz RJ / Wipf P ...Banerjee S / Bartesaghi A / Merk A / Rao P / Bulfer SL / Yan Y / Green N / Mroczkowski B / Neitz RJ / Wipf P / Falconieri V / Deshaies RJ / Milne JLS / Huryn D / Arkin M / Subramaniam S | |||||||||
引用 | ジャーナル: Science / 年: 2016 タイトル: 2.3 Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition. 著者: Soojay Banerjee / Alberto Bartesaghi / Alan Merk / Prashant Rao / Stacie L Bulfer / Yongzhao Yan / Neal Green / Barbara Mroczkowski / R Jeffrey Neitz / Peter Wipf / Veronica Falconieri / ...著者: Soojay Banerjee / Alberto Bartesaghi / Alan Merk / Prashant Rao / Stacie L Bulfer / Yongzhao Yan / Neal Green / Barbara Mroczkowski / R Jeffrey Neitz / Peter Wipf / Veronica Falconieri / Raymond J Deshaies / Jacqueline L S Milne / Donna Huryn / Michelle Arkin / Sriram Subramaniam / 要旨: p97 is a hexameric AAA+ adenosine triphosphatase (ATPase) that is an attractive target for cancer drug development. We report cryo-electron microscopy (cryo-EM) structures for adenosine diphosphate ...p97 is a hexameric AAA+ adenosine triphosphatase (ATPase) that is an attractive target for cancer drug development. We report cryo-electron microscopy (cryo-EM) structures for adenosine diphosphate (ADP)-bound, full-length, hexameric wild-type p97 in the presence and absence of an allosteric inhibitor at resolutions of 2.3 and 2.4 angstroms, respectively. We also report cryo-EM structures (at resolutions of ~3.3, 3.2, and 3.3 angstroms, respectively) for three distinct, coexisting functional states of p97 with occupancies of zero, one, or two molecules of adenosine 5'-O-(3-thiotriphosphate) (ATPγS) per protomer. A large corkscrew-like change in molecular architecture, coupled with upward displacement of the N-terminal domain, is observed only when ATPγS is bound to both the D1 and D2 domains of the protomer. These cryo-EM structures establish the sequence of nucleotide-driven structural changes in p97 at atomic resolution. They also enable elucidation of the binding mode of an allosteric small-molecule inhibitor to p97 and illustrate how inhibitor binding at the interface between the D1 and D2 domains prevents propagation of the conformational changes necessary for p97 function. | |||||||||
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_3298.map.gz | 73.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-3298-v30.xml emd-3298.xml | 11.8 KB 11.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_3298.png | 224.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-3298 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3298 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_3298_validation.pdf.gz | 334.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_3298_full_validation.pdf.gz | 333.6 KB | 表示 | |
XML形式データ | emd_3298_validation.xml.gz | 6.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3298 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3298 | 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_3298.map.gz / 形式: CCP4 / 大きさ: 78.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Reconstruction of human p97 bound to ATPgS (conformation II). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.676 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 : Full-length human p97 bound to ATPgS
全体 | 名称: Full-length human p97 bound to ATPgS |
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要素 |
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-超分子 #1000: Full-length human p97 bound to ATPgS
超分子 | 名称: Full-length human p97 bound to ATPgS / タイプ: sample / ID: 1000 / 詳細: The sample was monodisperse. / 集合状態: hexamer / Number unique components: 2 |
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分子量 | 理論値: 540 KDa / 手法: sequence |
-分子 #1: p97/VCP Transitional endoplasmic reticulum ATPase
分子 | 名称: p97/VCP Transitional endoplasmic reticulum ATPase / タイプ: protein_or_peptide / ID: 1 / Name.synonym: p97 / コピー数: 1 / 集合状態: hexamer / 組換発現: Yes |
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由来(天然) | 生物種: Homo sapiens (ヒト) / 別称: Human / 細胞中の位置: cytoplasm |
分子量 | 理論値: 540 KDa |
組換発現 | 生物種: Bacteria (unknown) / 組換細胞: E. coli / 組換プラスミド: Rosetta2 (DE3) |
配列 | UniProtKB: Transitional endoplasmic reticulum ATPase GO: ATP binding, signaling receptor binding, protein binding, lipid binding |
-分子 #2: Adenosine 5 gamma-thio triphosphate
分子 | 名称: Adenosine 5 gamma-thio triphosphate / タイプ: ligand / ID: 2 / Name.synonym: ATPgS / コピー数: 12 / 集合状態: monomer / 組換発現: No |
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由来(天然) | 生物種: unidentified (未定義) |
-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 | 0.9 mg/mL |
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緩衝液 | pH: 8 / 詳細: 25 mM Tris, 150 mM NaCl, 1 mM MgCl2, 1.0 mM TCEP |
グリッド | 詳細: 200 mesh Quantifoil R1.2/1/3 grids |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 90.15 K / 装置: FEI VITROBOT MARK IV / 手法: Blot for 2.5 seconds before plunging. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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温度 | 最低: 79.6 K / 最高: 79.8 K / 平均: 79.7 K |
特殊光学系 | エネルギーフィルター - 名称: Gatan, Inc. エネルギーフィルター - エネルギー下限: 0.0 eV エネルギーフィルター - エネルギー上限: 20.0 eV |
詳細 | Parallel beam illumination |
日付 | 2015年1月17日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 実像数: 628 / 平均電子線量: 40 e/Å2 詳細: Every image is the average of 40 frames recorded by the direct electron detector. |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 倍率(補正後): 36980 / 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): 2.7 µm / 最小 デフォーカス(公称値): 0.95 µm / 倍率(公称値): 105000 |
試料ステージ | 試料ホルダー: Liquid nitrogen cooled 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
CTF補正 | 詳細: each particle |
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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: 3.2 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: FREALIGN / 詳細: Map was corrected using a B-factor of -85 A^2. / 使用した粒子像数: 32406 |