+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-24531 | |||||||||
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タイトル | Cryo-EM structure of human p97 bound to CB-5083 and ADP. | |||||||||
マップデータ | Cryo-EM structure of human p97 bound to CB-5083 and ADP. | |||||||||
試料 |
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キーワード | p97 / VCP / TERA / Inhibitor / CB-5083 / HYDROLASE | |||||||||
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: 3.1 Å | |||||||||
データ登録者 | Caffrey B / Zhu X | |||||||||
引用 | ジャーナル: J Biol Chem / 年: 2021 タイトル: AAA+ ATPase p97/VCP mutants and inhibitor binding disrupt inter-domain coupling and subsequent allosteric activation. 著者: Brian Caffrey / Xing Zhu / Alison Berezuk / Katharine Tuttle / Sagar Chittori / Sriram Subramaniam / 要旨: The human AAA+ ATPase p97, also known as valosin-containing protein, a potential target for cancer therapeutics, plays a vital role in the clearing of misfolded proteins. p97 dysfunction is also ...The human AAA+ ATPase p97, also known as valosin-containing protein, a potential target for cancer therapeutics, plays a vital role in the clearing of misfolded proteins. p97 dysfunction is also known to play a crucial role in several neurodegenerative disorders, such as MultiSystem Proteinopathy 1 (MSP-1) and Familial Amyotrophic Lateral Sclerosis (ALS). However, the structural basis of its role in such diseases remains elusive. Here, we present cryo-EM structural analyses of four disease mutants p97, p97, p97, p97, as well as p97, implicated in resistance to the drug CB-5083, a potent p97 inhibitor. Our cryo-EM structures demonstrate that these mutations affect nucleotide-driven allosteric activation across the three principal p97 domains (N, D1, and D2) by predominantly interfering with either (1) the coupling between the D1 and N-terminal domains (p97 and p97), (2) the interprotomer interactions (p97), or (3) the coupling between D1 and D2 nucleotide domains (p97, p97). We also show that binding of the competitive inhibitor, CB-5083, to the D2 domain prevents conformational changes similar to those seen for mutations that affect coupling between the D1 and D2 domains. Our studies enable tracing of the path of allosteric activation across p97 and establish a common mechanistic link between active site inhibition and defects in allosteric activation by disease-causing mutations and have potential implications for the design of novel allosteric compounds that can modulate 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_24531.map.gz | 122.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-24531-v30.xml emd-24531.xml | 11.7 KB 11.7 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_24531_fsc.xml | 18.1 KB | 表示 | FSCデータファイル |
画像 | emd_24531.png | 53.7 KB | ||
Filedesc metadata | emd-24531.cif.gz | 5.7 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-24531 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24531 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_24531_validation.pdf.gz | 535.6 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_24531_full_validation.pdf.gz | 535.1 KB | 表示 | |
XML形式データ | emd_24531_validation.xml.gz | 11.9 KB | 表示 | |
CIF形式データ | emd_24531_validation.cif.gz | 16.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24531 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24531 | HTTPS FTP |
-関連構造データ
関連構造データ | 7rliMC 7rl6C 7rl7C 7rl9C 7rlaC 7rlbC 7rlcC 7rldC 7rlfC 7rlgC 7rlhC 7rljC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ |
-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_24531.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Cryo-EM structure of human p97 bound to CB-5083 and ADP. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1 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 Dodecameric p97 bound to ADP in the D1 domain and CB-...
全体 | 名称: Full-length Dodecameric p97 bound to ADP in the D1 domain and CB-5083 in the D2 domain. |
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要素 |
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-超分子 #1: Full-length Dodecameric p97 bound to ADP in the D1 domain and CB-...
超分子 | 名称: Full-length Dodecameric p97 bound to ADP in the D1 domain and CB-5083 in the D2 domain. タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1 |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 540 KDa |
-分子 #1: Transitional endoplasmic reticulum ATPase
分子 | 名称: Transitional endoplasmic reticulum ATPase / タイプ: protein_or_peptide / ID: 1 / コピー数: 12 / 光学異性体: LEVO / EC番号: vesicle-fusing ATPase |
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由来(天然) | 生物種: Homo sapiens (ヒト) |
分子量 | 理論値: 91.231648 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: HHHHHHGTSE NLYFQGASGA DSKGDDLSTA ILKQKNRPNR LIVDEAINED NSVVSLSQPK MDELQLFRGD TVLLKGKKRR EAVCIVLSD DTCSDEKIRM NRVVRNNLRV RLGDVISIQP CPDVKYGKRI HVLPIDDTVE GITGNLFEVY LKPYFLEAYR P IRKGDIFL ...文字列: HHHHHHGTSE NLYFQGASGA DSKGDDLSTA ILKQKNRPNR LIVDEAINED NSVVSLSQPK MDELQLFRGD TVLLKGKKRR EAVCIVLSD DTCSDEKIRM NRVVRNNLRV RLGDVISIQP CPDVKYGKRI HVLPIDDTVE GITGNLFEVY LKPYFLEAYR P IRKGDIFL VRGGMRAVEF KVVETDPSPY CIVAPDTVIH CEGEPIKRED EEESLNEVGY DDIGGCRKQL AQIKEMVELP LR HPALFKA IGVKPPRGIL LYGPPGTGKT LIARAVANET GAFFFLINGP EIMSKLAGES ESNLRKAFEE AEKNAPAIIF IDE LDAIAP KREKTHGEVE RRIVSQLLTL MDGLKQRAHV IVMAATNRPN SIDPALRRFG RFDREVDIGI PDATGRLEIL QIHT KNMKL ADDVDLEQVA NETHGHVGAD LAALCSEAAL QAIRKKMDLI DLEDETIDAE VMNSLAVTMD DFRWALSQSN PSALR ETVV EVPQVTWEDI GGLEDVKREL QELVQYPVEH PDKFLKFGMT PSKGVLFYGP PGCGKTLLAK AIANECQANF ISIKGP ELL TMWFGESEAN VREIFDKARQ AAPCVLFFDE LDSIAKARGG NIGDGGGAAD RVINQILTEM DGMSTKKNVF IIGATNR PD IIDPAILRPG RLDQLIYIPL PDEKSRVAIL KANLRKSPVA KDVDLEFLAK MTNGFSGADL TEICQRACKL AIRESIES E IRRERERQTN PSAMEVEEDD PVPEIRRDHF EEAMRFARRS VSDNDIRKYE MFAQTLQQSR GFGSFRFPSG NQGGAGPSQ GSGGGTGGSV YTEDNDDDLY G UniProtKB: Transitional endoplasmic reticulum ATPase |
-分子 #2: 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-...
分子 | 名称: 1-[4-(benzylamino)-7,8-dihydro-5H-pyrano[4,3-d]pyrimidin-2-yl]-2-methyl-1H-indole-4-carboxamide タイプ: ligand / ID: 2 / コピー数: 12 / 式: JDP |
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分子量 | 理論値: 413.472 Da |
Chemical component information | ChemComp-JDP: |
-分子 #3: ADENOSINE-5'-DIPHOSPHATE
分子 | 名称: ADENOSINE-5'-DIPHOSPHATE / タイプ: ligand / ID: 3 / コピー数: 12 / 式: ADP |
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分子量 | 理論値: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-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 | 2D array |
-試料調製
濃度 | 2 mg/mL | |||||||||||||||
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緩衝液 | pH: 8 構成要素:
詳細: Protein Storage Buffer and CB-5083 | |||||||||||||||
凍結 | 凍結剤: ETHANE |
-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: FEI FALCON IV (4k x 4k) 実像数: 3600 / 平均電子線量: 40.0 e/Å2 |
電子線 | 加速電圧: 300 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |