+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9220 | ||||||||||||
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タイトル | Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome | ||||||||||||
マップデータ | The complete map of state EC2 of substrate-engaged human proteasome, low pass-filtered to 3 Angstrom without amplitude correction | ||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 positive regulation of inclusion body assembly / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / 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 / 減数分裂 / positive regulation of proteasomal protein catabolic process / metal-dependent deubiquitinase activity ...positive regulation of inclusion body assembly / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / 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 / 減数分裂 / positive regulation of proteasomal protein catabolic process / metal-dependent deubiquitinase activity / proteasome regulatory particle / purine ribonucleoside triphosphate binding / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein K63-linked deubiquitination / negative regulation of programmed cell death / regulation of endopeptidase activity / 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 / Homologous DNA Pairing and Strand Exchange / 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) / Somitogenesis / Impaired BRCA2 binding to RAD51 / K63-linked deubiquitinase activity / immune system process / myofibril / proteasome binding / regulation of protein catabolic process / proteasome storage granule / Presynaptic phase of homologous DNA pairing and strand exchange / blastocyst development / transcription factor binding / polyubiquitin modification-dependent protein binding / general transcription initiation factor binding / endopeptidase activator activity / NF-kappaB binding / proteasome assembly / proteasome endopeptidase complex / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / regulation of proteasomal protein catabolic process / enzyme regulator activity / mRNA export from nucleus / 封入体 / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / : / negative regulation of inflammatory response to antigenic stimulus / : / response to organonitrogen compound / sarcomere / proteolysis involved in protein catabolic process / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / 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 / Degradation of DVL / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / proteasomal protein catabolic process / 細胞分化 / P-body / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of GLI1 by the proteasome / lipopolysaccharide binding / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / Hedgehog ligand biogenesis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / double-strand break repair via homologous recombination / Vif-mediated degradation of APOBEC3G / G2/M Checkpoints / Hedgehog 'on' state / Autodegradation of the E3 ubiquitin ligase COP1 / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Regulation of RUNX3 expression and activity / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / response to virus 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) / Saccharomyces cerevisiae RM11-1a (パン酵母) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.6 Å | ||||||||||||
データ登録者 | Mao YD | ||||||||||||
資金援助 | 中国, 米国, 3件
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引用 | ジャーナル: Nature / 年: 2019 タイトル: Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome. 著者: Yuanchen Dong / Shuwen Zhang / Zhaolong Wu / Xuemei Li / Wei Li Wang / Yanan Zhu / Svetla Stoilova-McPhie / Ying Lu / Daniel Finley / Youdong Mao / 要旨: The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of ...The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of the substrate-engaged human proteasome in seven conformational states at 2.8-3.6 Å resolution, captured during breakdown of a polyubiquitylated protein. These structures illuminate a spatiotemporal continuum of dynamic substrate-proteasome interactions from ubiquitin recognition to substrate translocation, during which ATP hydrolysis sequentially navigates through all six ATPases. There are three principal modes of coordinated hydrolysis, featuring hydrolytic events in two oppositely positioned ATPases, in two adjacent ATPases and in one ATPase at a time. These hydrolytic modes regulate deubiquitylation, initiation of translocation and processive unfolding of substrates, respectively. Hydrolysis of ATP powers a hinge-like motion in each ATPase that regulates its substrate interaction. Synchronization of ATP binding, ADP release and ATP hydrolysis in three adjacent ATPases drives rigid-body rotations of substrate-bound ATPases that are propagated unidirectionally in the ATPase ring and unfold the substrate. | ||||||||||||
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_9220.map.gz | 748.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9220-v30.xml emd-9220.xml | 60.1 KB 60.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_9220.png | 99.6 KB | ||
その他 | emd_9220_additional_1.map.gz emd_9220_additional_2.map.gz | 751.1 MB 731.2 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9220 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9220 | HTTPS FTP |
-関連構造データ
関連構造データ | 6mshMC 9215C 9216C 9217C 9218C 9219C 9221C 9222C 9223C 9224C 9225C 9226C 9227C 9228C 9229C 6msbC 6msdC 6mseC 6msgC 6msjC 6mskC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
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類似構造データ | |
電子顕微鏡画像生データ | EMPIAR-10669 (タイトル: Cryo-EM dataset of the substrate-engaged human 26S proteasome Data size: 13.9 TB Data #1: Drift-corrected frame-averaged super-counting mode micrographs and extracted particles of substrate-engaged human 26S proteasome [micrographs - single frame]) |
-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_9220.map.gz / 形式: CCP4 / 大きさ: 824 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | The complete map of state EC2 of substrate-engaged human proteasome, low pass-filtered to 3 Angstrom without amplitude correction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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:
CCP4マップ ヘッダ情報:
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-添付データ
-追加マップ: The complete map of state EC2 of substrate-engaged...
ファイル | emd_9220_additional_1.map | ||||||||||||
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注釈 | The complete map of state EC2 of substrate-engaged human proteasome, low pass-filtered to 3.5 Angstrom with amplitude correction with 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, uncorrected raw EC2 map of complete holoenzyme
ファイル | emd_9220_additional_2.map | ||||||||||||
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注釈 | Unfiltered, uncorrected raw EC2 map of complete holoenzyme | ||||||||||||
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 : Proteasome
+超分子 #1: Proteasome
+分子 #1: 26S proteasome non-ATPase regulatory subunit 1
+分子 #2: 26S proteasome non-ATPase regulatory subunit 3
+分子 #3: 26S proteasome non-ATPase regulatory subunit 12
+分子 #4: 26S proteasome non-ATPase regulatory subunit 11
+分子 #5: 26S proteasome non-ATPase regulatory subunit 6
+分子 #6: 26S proteasome non-ATPase regulatory subunit 7
+分子 #7: 26S proteasome non-ATPase regulatory subunit 13
+分子 #8: 26S proteasome non-ATPase regulatory subunit 4
+分子 #9: 26S proteasome non-ATPase regulatory subunit 14
+分子 #10: 26S proteasome non-ATPase regulatory subunit 8
+分子 #11: 26S proteasome complex subunit SEM1
+分子 #12: 26S proteasome non-ATPase regulatory subunit 2
+分子 #13: 26S proteasome regulatory subunit 7
+分子 #14: 26S proteasome regulatory subunit 4
+分子 #15: 26S proteasome regulatory subunit 8
+分子 #16: 26S proteasome regulatory subunit 6B
+分子 #17: 26S proteasome regulatory subunit 10B
+分子 #18: 26S proteasome regulatory subunit 6A
+分子 #19: substrate
+分子 #20: Proteasome subunit alpha type-6
+分子 #21: Proteasome subunit alpha type-2
+分子 #22: Proteasome subunit alpha type-4
+分子 #23: Proteasome subunit alpha type-7
+分子 #24: Proteasome subunit alpha type-5
+分子 #25: Proteasome subunit alpha type-1
+分子 #26: Proteasome subunit alpha type-3
+分子 #27: Proteasome subunit beta type-6
+分子 #28: Proteasome subunit beta type-7
+分子 #29: Proteasome subunit beta type-3
+分子 #30: Proteasome subunit beta type-2
+分子 #31: Proteasome subunit beta type-5
+分子 #32: Proteasome subunit beta type-1
+分子 #33: Proteasome subunit beta type-4
+分子 #34: ZINC ION
+分子 #35: ADENOSINE-5'-TRIPHOSPHATE
+分子 #36: ADENOSINE-5'-DIPHOSPHATE
-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: 7.5 |
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グリッド | 詳細: unspecified |
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy |
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: 44.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期 角度割当 | タイプ: COMMON LINE |
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最終 角度割当 | タイプ: PROJECTION MATCHING |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.6 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 71651 |