+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-32272 | |||||||||
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タイトル | Structure of USP14-bound human 26S proteasome in state EA1_UBL | |||||||||
マップデータ | Complete map of the human proteasome holoenzyme in state EA1_UBL, with the RP/CP low-pass filtered to 3.3/2.8 angstrom and sharpened by a B-factor of -30/0 | |||||||||
試料 |
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キーワード | Proteasome / AAA-ATPase / Deubiquitinase / USP14 / HYDROLASE | |||||||||
機能・相同性 | 機能・相同性情報 negative regulation of ERAD pathway / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / meiosis I / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; オメガペプチターゼ / proteasome accessory complex / integrator complex / regulation of chemotaxis ...negative regulation of ERAD pathway / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / meiosis I / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; オメガペプチターゼ / proteasome accessory complex / integrator complex / regulation of chemotaxis / deubiquitinase activity / purine ribonucleoside triphosphate binding / protein K48-linked deubiquitination / proteasome regulatory particle / cytosolic proteasome complex / positive regulation of proteasomal protein catabolic process / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / negative regulation of programmed cell death / regulation of endopeptidase activity / protein K63-linked deubiquitination / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / : / K63-linked deubiquitinase activity / Somitogenesis / Impaired BRCA2 binding to RAD51 / endopeptidase inhibitor activity / myofibril / immune system process / proteasome binding / transcription factor binding / regulation of protein catabolic process / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / blastocyst development / general transcription initiation factor binding / NF-kappaB binding / endopeptidase activator activity / polyubiquitin modification-dependent protein binding / proteasome assembly / protein deubiquitination / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / mRNA export from nucleus / negative regulation of ubiquitin-dependent protein catabolic process / regulation of proteasomal protein catabolic process / enzyme regulator activity / inclusion body / sarcomere / proteasome complex / ciliary basal body / Regulation of activated PAK-2p34 by proteasome mediated degradation / proteolysis involved in protein catabolic process / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / stem cell differentiation / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Degradation of DVL / negative regulation of inflammatory response to antigenic stimulus / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / lipopolysaccharide binding / Hh mutants are degraded by ERAD / Degradation of AXIN / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / G2/M Checkpoints / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / double-strand break repair via homologous recombination / P-body / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / Degradation of GLI2 by the proteasome 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: 3.0 Å | |||||||||
データ登録者 | Zhang S / Zou S / Yin D / Wu Z / Mao Y | |||||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Nature / 年: 2022 タイトル: USP14-regulated allostery of the human proteasome by time-resolved cryo-EM. 著者: Shuwen Zhang / Shitao Zou / Deyao Yin / Lihong Zhao / Daniel Finley / Zhaolong Wu / Youdong Mao / 要旨: Proteasomal degradation of ubiquitylated proteins is tightly regulated at multiple levels. A primary regulatory checkpoint is the removal of ubiquitin chains from substrates by the deubiquitylating ...Proteasomal degradation of ubiquitylated proteins is tightly regulated at multiple levels. A primary regulatory checkpoint is the removal of ubiquitin chains from substrates by the deubiquitylating enzyme ubiquitin-specific protease 14 (USP14), which reversibly binds the proteasome and confers the ability to edit and reject substrates. How USP14 is activated and regulates proteasome function remain unknown. Here we present high-resolution cryo-electron microscopy structures of human USP14 in complex with the 26S proteasome in 13 distinct conformational states captured during degradation of polyubiquitylated proteins. Time-resolved cryo-electron microscopy analysis of the conformational continuum revealed two parallel pathways of proteasome state transitions induced by USP14, and captured transient conversion of substrate-engaged intermediates into substrate-inhibited intermediates. On the substrate-engaged pathway, ubiquitin-dependent activation of USP14 allosterically reprograms the conformational landscape of the AAA-ATPase motor and stimulates opening of the core particle gate, enabling observation of a near-complete cycle of asymmetric ATP hydrolysis around the ATPase ring during processive substrate unfolding. Dynamic USP14-ATPase interactions decouple the ATPase activity from RPN11-catalysed deubiquitylation and kinetically introduce three regulatory checkpoints on the proteasome, at the steps of ubiquitin recognition, substrate translocation initiation and ubiquitin chain recycling. These findings provide insights into the complete functional cycle of the USP14-regulated proteasome and establish mechanistic foundations for the discovery of USP14-targeted therapies. | |||||||||
履歴 |
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-構造の表示
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 | emd_32272.map.gz | 887.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-32272-v30.xml emd-32272.xml | 64.8 KB 64.8 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_32272.png | 76.4 KB | ||
Filedesc metadata | emd-32272.cif.gz | 14.8 KB | ||
その他 | emd_32272_additional_1.map.gz emd_32272_additional_2.map.gz emd_32272_additional_3.map.gz emd_32272_additional_4.map.gz | 868.6 MB 893.3 MB 870.7 MB 892.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-32272 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32272 | HTTPS FTP |
-関連構造データ
関連構造データ | 7w37MC 7w38C 7w39C 7w3aC 7w3bC 7w3cC 7w3fC 7w3gC 7w3hC 7w3iC 7w3jC 7w3kC 7w3mC 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 | 類似検索 - 機能・相同性F&H 検索 |
-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_32272.map.gz / 形式: CCP4 / 大きさ: 1000 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Complete map of the human proteasome holoenzyme in state EA1_UBL, with the RP/CP low-pass filtered to 3.3/2.8 angstrom and sharpened by a B-factor of -30/0 | ||||||||||||||||||||||||||||||||||||
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: 0.685 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-追加マップ: Unfiltered, unsharpened raw map of the human proteasome...
ファイル | emd_32272_additional_1.map | ||||||||||||
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注釈 | Unfiltered, unsharpened raw map of the human proteasome in state EA1_UBL after RP-masked refinement | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Map of the human proteasome in state EA1 UBL...
ファイル | emd_32272_additional_2.map | ||||||||||||
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注釈 | Map of the human proteasome in state EA1_UBL after RP-masked refinement, low-pass filtered to 3.3 angstrom and sharpened by a B-factor of -30 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Unfiltered, unsharpened raw map of the human proteasome...
ファイル | emd_32272_additional_3.map | ||||||||||||
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注釈 | Unfiltered, unsharpened raw map of the human proteasome in state EA1_UBL after CP-masked refinement | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Map of the human proteasome in state EA1 UBL...
ファイル | emd_32272_additional_4.map | ||||||||||||
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注釈 | Map of the human proteasome in state EA1_UBL after CP-masked refinement, low-pass filtered to 3.3 angstrom with no sharpening B-factor applied | ||||||||||||
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 : 26S proteasome
+超分子 #1: 26S proteasome
+分子 #1: 26S protease regulatory subunit 7
+分子 #2: 26S protease regulatory subunit 4
+分子 #3: Isoform 2 of 26S proteasome regulatory subunit 8
+分子 #4: 26S protease regulatory subunit 6B
+分子 #5: 26S proteasome regulatory subunit 10B
+分子 #6: 26S protease regulatory subunit 6A
+分子 #7: Proteasome subunit alpha type-6
+分子 #8: Proteasome subunit alpha type-2
+分子 #9: Proteasome subunit alpha type-4
+分子 #10: Proteasome subunit alpha type-7
+分子 #11: Proteasome subunit alpha type-5
+分子 #12: Isoform Long of Proteasome subunit alpha type-1
+分子 #13: Proteasome subunit alpha type-3
+分子 #14: Proteasome subunit beta type-6
+分子 #15: Proteasome subunit beta type-7
+分子 #16: Proteasome subunit beta type-3
+分子 #17: Proteasome subunit beta type-2
+分子 #18: Proteasome subunit beta type-5
+分子 #19: Proteasome subunit beta type-1
+分子 #20: Proteasome subunit beta type-4
+分子 #21: 26S proteasome non-ATPase regulatory subunit 1
+分子 #22: 26S proteasome non-ATPase regulatory subunit 3
+分子 #23: 26S proteasome non-ATPase regulatory subunit 12
+分子 #24: 26S proteasome non-ATPase regulatory subunit 11
+分子 #25: 26S proteasome non-ATPase regulatory subunit 6
+分子 #26: 26S proteasome non-ATPase regulatory subunit 7
+分子 #27: 26S proteasome non-ATPase regulatory subunit 13
+分子 #28: 26S proteasome non-ATPase regulatory subunit 4
+分子 #29: 26S proteasome non-ATPase regulatory subunit 14
+分子 #30: 26S proteasome non-ATPase regulatory subunit 8
+分子 #31: 26S proteasome non-ATPase regulatory subunit 2
+分子 #32: Ubiquitin carboxyl-terminal hydrolase 14
+分子 #33: 26S proteasome complex subunit DSS1
+分子 #34: ADENOSINE-5'-TRIPHOSPHATE
+分子 #35: MAGNESIUM ION
+分子 #36: ADENOSINE-5'-DIPHOSPHATE
+分子 #37: ZINC ION
-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
緩衝液 | pH: 7 |
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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: GATAN K2 SUMMIT (4k 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 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 5.0 µm / 最小 デフォーカス(公称値): 0.4 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: EMDB MAP EMDB ID: |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 367235 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |