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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-24302 | |||||||||
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タイトル | p47-bound p97-R155H mutant with ATPgammaS | |||||||||
![]() | p47-bound p97-R155H mutant with ATPgammaS | |||||||||
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![]() | AAA+ ATPase / MOTOR PROTEIN / HYDROLASE / HYDROLASE-Lipid Binding Protein complex | |||||||||
機能・相同性 | ![]() negative regulation of protein localization to centrosome / RHOH GTPase cycle / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / positive regulation of Lys63-specific deubiquitinase activity / Golgi stack / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair ...negative regulation of protein localization to centrosome / RHOH GTPase cycle / positive regulation of mitotic centrosome separation / nuclear membrane reassembly / positive regulation of Lys63-specific deubiquitinase activity / Golgi stack / flavin adenine dinucleotide catabolic process / positive regulation of oxidative phosphorylation / VCP-NSFL1C complex / protein-DNA covalent cross-linking repair / endoplasmic reticulum stress-induced pre-emptive quality control / endosome to lysosome transport via multivesicular body sorting pathway / cellular response to arsenite ion / spindle pole centrosome / Derlin-1 retrotranslocation complex / BAT3 complex binding / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / NADH metabolic process / cellular response to misfolded protein / stress granule disassembly / K48-linked polyubiquitin modification-dependent protein binding / positive regulation of mitochondrial membrane potential / negative regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / 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 / Golgi organization / establishment of mitotic spindle orientation / RHOH GTPase cycle / autophagosome maturation / autophagosome assembly / HSF1 activation / polyubiquitin modification-dependent protein binding / proteasomal protein catabolic process / Protein methylation / endoplasmic reticulum to Golgi vesicle-mediated transport / translesion synthesis / interstrand cross-link repair / negative regulation of smoothened signaling pathway / ERAD pathway / ATP metabolic process / endoplasmic reticulum unfolded protein response / Attachment and Entry / viral genome replication / proteasome complex / lipid droplet / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / Hh mutants are degraded by ERAD / macroautophagy / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / positive regulation of protein-containing complex assembly / establishment of protein localization / ABC-family proteins mediated transport / ADP binding / autophagy / Aggrephagy / cytoplasmic stress granule / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of protein catabolic process / activation of cysteine-type endopeptidase activity involved in apoptotic process / KEAP1-NFE2L2 pathway / azurophil granule lumen / double-strand break repair / Ovarian tumor domain proteases / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / Neddylation / chromosome / site of double-strand break / cellular response to heat / ATPase binding / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / protein phosphatase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / secretory granule lumen / ficolin-1-rich granule lumen / membrane fusion / Attachment and Entry / protein ubiquitination / protein domain specific binding / intracellular membrane-bounded organelle / DNA repair 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.23 Å | |||||||||
![]() | Nandi P / Li S | |||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Structural and Functional Analysis of Disease-Linked p97 ATPase Mutant Complexes. 著者: Purbasha Nandi / Shan Li / Rod Carlo A Columbres / Feng Wang / Dewight R Williams / Yu-Ping Poh / Tsui-Fen Chou / Po-Lin Chiu / ![]() 要旨: IBMPFD/ALS is a genetic disorder caused by a single amino acid mutation on the p97 ATPase, promoting ATPase activity and cofactor dysregulation. The disease mechanism underlying p97 ATPase ...IBMPFD/ALS is a genetic disorder caused by a single amino acid mutation on the p97 ATPase, promoting ATPase activity and cofactor dysregulation. The disease mechanism underlying p97 ATPase malfunction remains unclear. To understand how the mutation alters the ATPase regulation, we assembled a full-length p97 with its p47 cofactor and first visualized their structures using single-particle cryo-EM. More than one-third of the population was the dodecameric form. Nucleotide presence dissociates the dodecamer into two hexamers for its highly elevated function. The N-domains of the p97 mutant all show up configurations in ADP- or ATPS-bound states. Our functional and structural analyses showed that the p47 binding is likely to impact the p97 ATPase activities via changing the conformations of arginine fingers. These functional and structural analyses underline the ATPase dysregulation with the miscommunication between the functional modules of the p97. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 49.8 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 15.9 KB 15.9 KB | 表示 表示 | ![]() |
画像 | ![]() | 74.7 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 538.6 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 538.2 KB | 表示 | |
XML形式データ | ![]() | 6.2 KB | 表示 | |
CIF形式データ | ![]() | 7 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 7r7sMC ![]() 7l5wC ![]() 7l5xC ![]() 7r7tC ![]() 7r7uC 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 ( |
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類似構造データ | |
電子顕微鏡画像生データ | ![]() Data size: 280.3 Data #1: Motion corrected dose-weighted micrographs for the cryo-EM dataset of disease mutant p97R155H-p47 in presence of ADP. [micrographs - single frame]) |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | p47-bound p97-R155H mutant with ATPgammaS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.413 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
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試料の構成要素
-全体 : p47-bound p97-R155H mutant with ATPgammaS
全体 | 名称: p47-bound p97-R155H mutant with ATPgammaS |
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要素 |
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-超分子 #1: p47-bound p97-R155H mutant with ATPgammaS
超分子 | 名称: p47-bound p97-R155H mutant with ATPgammaS / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1-#2 / 詳細: p47-bound p97-R155H mutant with ATPgammaS |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 723 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: 6 / 光学異性体: LEVO / EC番号: vesicle-fusing ATPase |
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由来(天然) | 生物種: ![]() |
分子量 | 理論値: 89.417773 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVHGGMR A VEFKVVET ...文字列: MASGADSKGD DLSTAILKQK NRPNRLIVDE AINEDNSVVS LSQPKMDELQ LFRGDTVLLK GKKRREAVCI VLSDDTCSDE KIRMNRVVR NNLRVRLGDV ISIQPCPDVK YGKRIHVLPI DDTVEGITGN LFEVYLKPYF LEAYRPIRKG DIFLVHGGMR A VEFKVVET DPSPYCIVAP DTVIHCEGEP IKREDEEESL NEVGYDDIGG CRKQLAQIKE MVELPLRHPA LFKAIGVKPP RG ILLYGPP GTGKTLIARA VANETGAFFF LINGPEIMSK LAGESESNLR KAFEEAEKNA PAIIFIDELD AIAPKREKTH GEV ERRIVS QLLTLMDGLK QRAHVIVMAA TNRPNSIDPA LRRFGRFDRE VDIGIPDATG RLEILQIHTK NMKLADDVDL EQVA NETHG HVGADLAALC SEAALQAIRK KMDLIDLEDE TIDAEVMNSL AVTMDDFRWA LSQSNPSALR ETVVEVPQVT WEDIG GLED VKRELQELVQ YPVEHPDKFL KFGMTPSKGV LFYGPPGCGK TLLAKAIANE CQANFISIKG PELLTMWFGE SEANVR EIF DKARQAAPCV LFFDELDSIA KARGGNIGDG GGAADRVINQ ILTEMDGMST KKNVFIIGAT NRPDIIDPAI LRPGRLD QL IYIPLPDEKS RVAILKANLR KSPVAKDVDL EFLAKMTNGF SGADLTEICQ RACKLAIRES IESEIRRERE RQTNPSAM E VEEDDPVPEI RRDHFEEAMR FARRSVSDND IRKYEMFAQT LQQSRGFGSF RFPSGNQGGA GPSQGSGGGT GGSVYTEDN DDDLYG UniProtKB: Transitional endoplasmic reticulum ATPase |
-分子 #2: NSFL1 cofactor p47
分子 | 名称: NSFL1 cofactor p47 / タイプ: protein_or_peptide / ID: 2 / コピー数: 2 / 光学異性体: LEVO |
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由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 40.731855 KDa |
組換発現 | 生物種: ![]() ![]() |
配列 | 文字列: MAEERQDALR EFVAVTGAEE DRARFFLESA GWDLQIALAS FYEDGGDEDI VTISQATPSS VSRGTAPSDN RVTSFRDLIH DQDEEEEEE EGQRFYAGGS ERSGQQIVGP PRKKSPNELV DDLFKGAKEH GAVAVERVTK SPGETSKPRP FAGGGYRLGA A PEEESAYV ...文字列: MAEERQDALR EFVAVTGAEE DRARFFLESA GWDLQIALAS FYEDGGDEDI VTISQATPSS VSRGTAPSDN RVTSFRDLIH DQDEEEEEE EGQRFYAGGS ERSGQQIVGP PRKKSPNELV DDLFKGAKEH GAVAVERVTK SPGETSKPRP FAGGGYRLGA A PEEESAYV AGERRRHSGQ DVHVVLKLWK TGFSLDNGDL RSYQDPSNAQ FLESIRRGEV PAELRRLAHG GQVNLDMEDH RD EDFVKPK GAFKAFTGEG QKLGSTAPQV LNTSSPAQQA ENEAKASSSI LINEAEPTTN IQIRLADGGR LVQKFNHSHR ISD IRLFIV DARPAMAATS FVLMTTFPNK ELADENQTLK EANLLNAVIV QRLT UniProtKB: NSFL1 cofactor p47 |
-分子 #3: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
分子 | 名称: PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / タイプ: ligand / ID: 3 / コピー数: 12 / 式: AGS |
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分子量 | 理論値: 523.247 Da |
Chemical component information | ![]() ChemComp-AGS: |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
濃度 | 0.2 mg/mL | ||||||||||||
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緩衝液 | pH: 7.4 構成要素:
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グリッド | モデル: C-flat-2/1 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY ARRAY | ||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 292 K / 装置: FEI VITROBOT MARK IV / 詳細: The grid was blotted for 6 seconds.. | ||||||||||||
詳細 | The protein sample was monodisperse. |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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アライメント法 | Coma free - Residual tilt: 0.001 mrad |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 実像数: 2796 / 平均電子線量: 44.4 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | C2レンズ絞り径: 50.0 µm / 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): -2.5 µm / 最小 デフォーカス(公称値): -0.8 µm / 倍率(公称値): 48077 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |