+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-23458 | |||||||||
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タイトル | Human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos in the presence of ATP and sub-stoichiometric NMS-873 (Class 6) | |||||||||
マップデータ | ||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 positive regulation of Lys63-specific deubiquitinase activity / 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 Lys63-specific deubiquitinase activity / 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 / aggresome assembly / VCP-NPL4-UFD1 AAA ATPase complex / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / vesicle-fusing ATPase / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / K48-linked polyubiquitin modification-dependent protein binding / retrograde protein transport, ER to cytosol / regulation of aerobic respiration / positive regulation of ATP biosynthetic process / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / ubiquitin-like protein ligase binding / MHC class I protein binding / autophagosome maturation / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / HSF1 activation / proteasomal protein catabolic process / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / Protein methylation / interstrand cross-link repair / ERAD pathway / ATP metabolic process / negative regulation of smoothened signaling 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 / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / establishment of protein localization / positive regulation of non-canonical NF-kappaB signal transduction / ABC-family proteins mediated transport / activation of cysteine-type endopeptidase activity involved in apoptotic process / ADP binding / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of canonical Wnt signaling pathway / positive regulation of protein catabolic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / site of double-strand break / cellular response to heat / protein phosphatase binding / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / regulation of apoptotic process / ficolin-1-rich granule lumen / Attachment and Entry / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair / DNA damage response / ubiquitin protein ligase binding / lipid binding / glutamatergic synapse / endoplasmic reticulum membrane / Neutrophil degranulation / perinuclear region of cytoplasm / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / RNA binding / extracellular exosome / extracellular region 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.65 Å | |||||||||
データ登録者 | Pan M / Yu Y / Liu L / Zhao M | |||||||||
引用 | ジャーナル: Nat Struct Mol Biol / 年: 2021 タイトル: Mechanistic insight into substrate processing and allosteric inhibition of human p97. 著者: Man Pan / Yuanyuan Yu / Huasong Ai / Qingyun Zheng / Yuan Xie / Lei Liu / Minglei Zhao / 要旨: p97 processes ubiquitinated substrates and plays a central role in cellular protein homeostasis. Here, we report a series of cryo-EM structures of the substrate-engaged human p97 complex with ...p97 processes ubiquitinated substrates and plays a central role in cellular protein homeostasis. Here, we report a series of cryo-EM structures of the substrate-engaged human p97 complex with resolutions ranging from 2.9 to 3.8 Å that captured 'power-stroke'-like motions of both the D1 and D2 ATPase rings of p97. A key feature of these structures is the critical conformational changes of the intersubunit signaling (ISS) motifs, which tighten the binding of nucleotides and neighboring subunits and contribute to the spiral staircase conformation of the D1 and D2 rings. In addition, we determined the cryo-EM structure of human p97 in complex with NMS-873, a potent p97 inhibitor, at a resolution of 2.4 Å. The structures showed that NMS-873 binds at a cryptic groove in the D2 domain and interacts with the ISS motif, preventing its conformational change and thus blocking substrate translocation allosterically. | |||||||||
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_23458.map.gz | 97.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-23458-v30.xml emd-23458.xml | 20.3 KB 20.3 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_23458_fsc.xml | 11.4 KB | 表示 | FSCデータファイル |
画像 | emd_23458.png | 183.8 KB | ||
マスクデータ | emd_23458_msk_1.map | 125 MB | マスクマップ | |
その他 | emd_23458_additional_1.map.gz emd_23458_half_map_1.map.gz emd_23458_half_map_2.map.gz | 115.4 MB 98.4 MB 98.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-23458 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23458 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_23458_validation.pdf.gz | 560.2 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_23458_full_validation.pdf.gz | 559.8 KB | 表示 | |
XML形式データ | emd_23458_validation.xml.gz | 18.7 KB | 表示 | |
CIF形式データ | emd_23458_validation.cif.gz | 24.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23458 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23458 | 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_23458.map.gz / 形式: CCP4 / 大きさ: 125 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 1.063 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
-マスク #1
ファイル | emd_23458_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: #1
ファイル | emd_23458_additional_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_23458_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_23458_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
-全体 : Human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos ...
全体 | 名称: Human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos in the presence of ATP and sub-stoichiometric NMS-873 |
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要素 |
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-超分子 #1: Human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos ...
超分子 | 名称: Human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos in the presence of ATP and sub-stoichiometric NMS-873 タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: all |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Escherichia coli K-12 (大腸菌) |
-分子 #1: Human p97 (A232E/E578Q)
分子 | 名称: Human p97 (A232E/E578Q) / タイプ: protein_or_peptide / ID: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
組換発現 | 生物種: Escherichia coli K-12 (大腸菌) |
配列 | 文字列: MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVC IVLSDDTCSD EKIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI D DTVEGITG NLFEVYLKPY FLEAYRPIRK GDIFLVRGGM RAVEFKVVET ...文字列: MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVC IVLSDDTCSD EKIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI D DTVEGITG NLFEVYLKPY FLEAYRPIRK GDIFLVRGGM RAVEFKVVET DPSPYCIVAP DT VIHCEGE PIKREDEEES LNEVGYDDIG GCRKQLAQIK EMVELPLRHP ALFKEIGVKP PRG ILLYGP PGTGKTLIAR AVANETGAFF FLINGPEIMS KLAGESESNL RKAFEEAEKN APAI IFIDE LDAIAPKREK THGEVERRIV SQLLTLMDGL KQRAHVIVMA ATNRPNSIDP ALRRF GRFD REVDIGIPDA TGRLEILQIH TKNMKLADDV DLEQVANETH GHVGADLAAL CSEAAL QAI RKKMDLIDLE DETIDAEVMN SLAVTMDDFR WALSQSNPSA LRETVVEVPQ VTWEDIG GL EDVKRELQEL VQYPVEHPDK FLKFGMTPSK GVLFYGPPGC GKTLLAKAIA NECQANFI S IKGPELLTMW FGESEANVRE IFDKARQAAP CVLFFDQLDS IAKARGGNIG DGGGAADRV INQILTEMDG MSTKKNVFII GATNRPDIID PAILRPGRLD QLIYIPLPDE KSRVAILKAN LRKSPVAKD VDLEFLAKMT NGFSGADLTE ICQRACKLAI RESIESEIRR ERERQTNPSA M EVEEDDPV PEIRRDHFEE AMRFARRSVS DNDIRKYEMF AQTLQQSRGF GSFRFPSGNQ GG AGPSQGS GGGTGGSVYT EDNDDDLYG |
-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 | 2.5 mg/mL |
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緩衝液 | pH: 8 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 281 K |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 50.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: AB INITIO MODEL |
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