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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-9222 | ||||||||||||
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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 ED2 of substrate-engaged human proteasome, low pass-filtered to 3 Angstrom without amplitude correction | ||||||||||||
試料 |
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キーワード | Proteosome / HYDROLASE | ||||||||||||
| 機能・相同性 | 機能・相同性情報thyrotropin-releasing hormone receptor binding / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear proteasome complex / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / integrator complex / proteasome accessory complex / meiosis I / purine ribonucleoside triphosphate binding ...thyrotropin-releasing hormone receptor binding / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / nuclear proteasome complex / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / integrator complex / proteasome accessory complex / meiosis I / purine ribonucleoside triphosphate binding / proteasome regulatory particle / cytosolic proteasome complex / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / Antigen processing: Ub, ATP-independent proteasomal degradation / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / sperm glycocalyx / protein K63-linked deubiquitination / negative regulation of programmed cell death / metal-dependent deubiquitinase activity / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / proteasome core complex / perinuclear theca / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / K63-linked deubiquitinase activity / transcription factor binding / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / proteasome binding / Impaired BRCA2 binding to RAD51 / myofibril / regulation of protein catabolic process / proteasome storage granule / proteasomal ubiquitin-independent protein catabolic process / sperm head-tail coupling apparatus / Presynaptic phase of homologous DNA pairing and strand exchange / general transcription initiation factor binding / protein deubiquitination / positive regulation of RNA polymerase II transcription preinitiation complex assembly / blastocyst development / polyubiquitin modification-dependent protein binding / immune system process / proteasome endopeptidase complex / NF-kappaB binding / proteasome core complex, beta-subunit complex / endopeptidase activator activity / threonine-type endopeptidase activity / proteasome assembly / mRNA export from nucleus / proteasome core complex, alpha-subunit complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / enzyme regulator activity / ERAD pathway / regulation of proteasomal protein catabolic process / inclusion body / ciliary tip / : / TBP-class protein binding / proteasome complex / stem cell differentiation / Regulation of activated PAK-2p34 by proteasome mediated degradation / sarcomere / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / ubiquitin binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / centriole / sperm end piece / P-body / negative regulation of inflammatory response to antigenic stimulus / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / lipopolysaccharide binding / Degradation of DVL / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Hedgehog ligand biogenesis / Degradation of GLI1 by the proteasome / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of RUNX3 expression and activity / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 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: 3.2 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: SurfView Molmil Jmol/JSmol |
| 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_9222.map.gz | 742.4 MB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-9222-v30.xml emd-9222.xml | 62.8 KB 62.8 KB | 表示 表示 | EMDBヘッダ |
| 画像 | emd_9222.png | 55 KB | ||
| Filedesc metadata | emd-9222.cif.gz | 14.7 KB | ||
| その他 | emd_9222_additional_1.map.gz emd_9222_additional_2.map.gz | 750.2 MB 730.9 MB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9222 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9222 | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 6mskMC ![]() 9215C ![]() 9216C ![]() 9217C ![]() 9218C ![]() 9219C ![]() 9220C ![]() 9221C ![]() 9223C ![]() 9224C ![]() 9225C ![]() 9226C ![]() 9227C ![]() 9228C ![]() 9229C ![]() 6msbC ![]() 6msdC ![]() 6mseC ![]() 6msgC ![]() 6mshC ![]() 6msjC C: 同じ文献を引用 ( 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 proteasomeData 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]) |
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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 |
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マップ
| ファイル | ダウンロード / ファイル: emd_9222.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 ED2 of substrate-engaged human proteasome, low pass-filtered to 3 Angstrom without amplitude correction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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:
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 ED2 of substrate-engaged...
| ファイル | emd_9222_additional_1.map | ||||||||||||
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| 注釈 | The complete map of state ED2 of substrate-engaged human proteasome, low pass-filtered to 3 Angstrom with amplitude correction with a B-factor of -40 | ||||||||||||
| 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 ED2 map of complete holoenzyme
| ファイル | emd_9222_additional_2.map | ||||||||||||
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| 注釈 | Unfiltered, uncorrected raw ED2 map of complete holoenzyme | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
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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: Rpt2, NP_002793.2 (26SHA chain B)
+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: MAGNESIUM ION
+分子 #37: 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 |
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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 |
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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: 44.0 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 |
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画像解析
| 初期モデル | モデルのタイプ: NONE |
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| 最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 348646 |
| 初期 角度割当 | タイプ: COMMON LINE |
| 最終 角度割当 | タイプ: PROJECTION MATCHING |
ムービー
コントローラー
万見について



キーワード
Homo sapiens (ヒト)
データ登録者
中国,
米国, 3件
引用
UCSF Chimera





































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