+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 8b5r | ||||||||||||
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タイトル | p97-p37-SPI substrate complex | ||||||||||||
要素 |
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キーワード | CHAPERONE (シャペロン) / AAA+ ATPase / p97 / VCP / Cdc48 / unfoldase / protein phosphatase-1 (プロテインホスファターゼ) / protein maturation | ||||||||||||
機能・相同性 | 機能・相同性情報 negative regulation of protein localization to centrosome / PTW/PP1 phosphatase complex / positive regulation of mitotic centrosome separation / regulation of nucleocytoplasmic transport / nuclear membrane reassembly / protein phosphatase 1 binding / protein phosphatase regulator activity / lamin binding / positive regulation of Lys63-specific deubiquitinase activity / flavin adenine dinucleotide catabolic process ...negative regulation of protein localization to centrosome / PTW/PP1 phosphatase complex / positive regulation of mitotic centrosome separation / regulation of nucleocytoplasmic transport / nuclear membrane reassembly / protein phosphatase 1 binding / protein phosphatase regulator activity / lamin binding / 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 / protein-DNA covalent cross-linking repair / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / endoplasmic reticulum stress-induced pre-emptive quality control / cellular response to arsenite ion / Derlin-1 retrotranslocation complex / BAT3 complex binding / spindle pole centrosome / positive regulation of protein K63-linked deubiquitination / deubiquitinase activator activity / mitotic spindle disassembly / VCP-NPL4-UFD1 AAA ATPase complex / aggresome assembly / regulation of protein localization to chromatin / vesicle-fusing ATPase / 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 / 微小管形成中心 / retrograde protein transport, ER to cytosol / Maturation of hRSV A proteins / regulation of aerobic respiration / myosin phosphatase activity / ATPase complex / protein serine/threonine phosphatase activity / glycogen metabolic process / regulation of synapse organization / ubiquitin-specific protease binding / protein-serine/threonine phosphatase / positive regulation of ATP biosynthetic process / Golgi organization / ERAD pathway / Triglyceride catabolism / ubiquitin-like protein ligase binding / entrainment of circadian clock by photoperiod / phosphatase activity / MHC class I protein binding / establishment of mitotic spindle orientation / phosphoprotein phosphatase activity / autophagosome maturation / 分裂溝 / blastocyst development / RHOH GTPase cycle / autophagosome assembly / polyubiquitin modification-dependent protein binding / HSF1 activation / DNA修復 / Protein methylation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / endoplasmic reticulum to Golgi vesicle-mediated transport / interstrand cross-link repair / enzyme regulator activity / negative regulation of smoothened signaling pathway / ATP metabolic process / Attachment and Entry / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / endoplasmic reticulum unfolded protein response / positive regulation of protein dephosphorylation / positive regulation of glial cell proliferation / Resolution of Sister Chromatid Cohesion / viral genome replication / lipid droplet / proteasome complex / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / proteasomal protein catabolic process / Josephin domain DUBs / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / ubiquitin binding / RHO GTPases Activate Formins / Hh mutants are degraded by ERAD / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / オートファジー / Translesion Synthesis by POLH / RAF activation / circadian regulation of gene expression / positive regulation of protein-containing complex assembly / ABC-family proteins mediated transport / establishment of protein localization / neuron differentiation / regulation of circadian rhythm 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) | ||||||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.1 Å | ||||||||||||
データ登録者 | van den Boom, J. / Marini, G. / Meyer, H. / Saibil, H. | ||||||||||||
資金援助 | 英国, 3件
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引用 | ジャーナル: EMBO J / 年: 2023 タイトル: Structural basis of ubiquitin-independent PP1 complex disassembly by p97. 著者: Johannes van den Boom / Guendalina Marini / Hemmo Meyer / Helen R Saibil / 要旨: The AAA+-ATPase p97 (also called VCP or Cdc48) unfolds proteins and disassembles protein complexes in numerous cellular processes, but how substrate complexes are loaded onto p97 and disassembled is ...The AAA+-ATPase p97 (also called VCP or Cdc48) unfolds proteins and disassembles protein complexes in numerous cellular processes, but how substrate complexes are loaded onto p97 and disassembled is unclear. Here, we present cryo-EM structures of p97 in the process of disassembling a protein phosphatase-1 (PP1) complex by extracting an inhibitory subunit from PP1. We show that PP1 and its partners SDS22 and inhibitor-3 (I3) are loaded tightly onto p97, surprisingly via a direct contact of SDS22 with the p97 N-domain. Loading is assisted by the p37 adapter that bridges two adjacent p97 N-domains underneath the substrate complex. A stretch of I3 is threaded into the central channel of the spiral-shaped p97 hexamer, while other elements of I3 are still attached to PP1. Thus, our data show how p97 arranges a protein complex between the p97 N-domain and central channel, suggesting a hold-and-extract mechanism for p97-mediated disassembly. | ||||||||||||
履歴 |
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-構造の表示
構造ビューア | 分子: MolmilJmol/JSmol |
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-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 8b5r.cif.gz | 672.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb8b5r.ent.gz | 458.2 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 8b5r.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/b5/8b5r ftp://data.pdbj.org/pub/pdb/validation_reports/b5/8b5r | HTTPS FTP |
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-関連構造データ
関連構造データ | 15861MC C: 同じ文献を引用 (文献) M: このデータのモデリングに利用したマップデータ |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-タンパク質 , 3種, 8分子 ABCDEFPS
#1: タンパク質 | 分子量: 90265.695 Da / 分子数: 6 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: VCP / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: P55072, vesicle-fusing ATPase #3: タンパク質 | | 分子量: 37030.777 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PPP1CC / 発現宿主: Trichoplusia ni (イラクサキンウワバ) 参照: UniProt: P36873, protein-serine/threonine phosphatase #4: タンパク質 | | 分子量: 41616.129 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: PPP1R7, SDS22 / 発現宿主: Trichoplusia ni (イラクサキンウワバ) / 参照: UniProt: Q15435 |
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-タンパク質・ペプチド , 1種, 1分子 I
#2: タンパク質・ペプチド | 分子量: 1890.321 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 発現宿主: Trichoplusia ni (イラクサキンウワバ) |
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-UBX domain-containing protein ... , 2種, 2分子 XY
#5: タンパク質・ペプチド | 分子量: 1123.238 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBXN2B 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: Q14CS0 |
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#6: タンパク質 | 分子量: 9759.220 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: UBXN2B 発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌) 参照: UniProt: Q14CS0 |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: p97 complex with p37 adaptor and SPI substrate / タイプ: COMPLEX / Entity ID: #1-#4, #6, #5 / 由来: RECOMBINANT |
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分子量 | 実験値: NO |
由来(天然) | 生物種: Homo sapiens (ヒト) |
由来(組換発現) | 生物種: Trichoplusia ni (イラクサキンウワバ) |
緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 300 divisions/in. / グリッドのタイプ: C-flat-1.2/1.3 |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 85 % / 凍結前の試料温度: 277 K |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 81000 X / 最大 デフォーカス(公称値): 3300 nm / 最小 デフォーカス(公称値): 1800 nm / アライメント法: BASIC |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 3 sec. / 電子線照射量: 48 e/Å2 フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) |
電子光学装置 | エネルギーフィルター名称: GIF Bioquantum / エネルギーフィルタースリット幅: 20 eV |
-解析
EMソフトウェア | 名称: PHENIX / バージョン: 1.20.1_4487: / カテゴリ: モデル精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3次元再構成 | 解像度: 6.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 191477 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT | ||||||||||||||||||||||||
拘束条件 |
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