+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-14084 | ||||||||||||||||||
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タイトル | 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state | ||||||||||||||||||
マップデータ | |||||||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 SAGA complex localization to transcription regulatory region / mitochondria-associated ubiquitin-dependent protein catabolic process / peroxisome fission / negative regulation of proteasomal protein catabolic process / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / nonfunctional rRNA decay ...SAGA complex localization to transcription regulatory region / mitochondria-associated ubiquitin-dependent protein catabolic process / peroxisome fission / negative regulation of proteasomal protein catabolic process / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / nonfunctional rRNA decay / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / protein-containing complex localization / mitochondrial fission / proteasome regulatory particle, base subcomplex / hypothalamus gonadotrophin-releasing hormone neuron development / K48-linked polyubiquitin modification-dependent protein binding / female meiosis I / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / fat pad development / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / proteasomal ubiquitin-independent protein catabolic process / peptide catabolic process / female gonad development / proteasome binding / seminiferous tubule development / regulation of protein catabolic process / male meiosis I / protein deubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / proteasome storage granule / : / endopeptidase activator activity / Ub-specific processing proteases / polyubiquitin modification-dependent protein binding / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / mRNA export from nucleus / enzyme regulator activity / energy homeostasis / regulation of neuron apoptotic process / regulation of proteasomal protein catabolic process / protein folding chaperone / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Evasion by RSV of host interferon responses / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / グリコーゲン合成 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / Neutrophil degranulation / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) / baker's yeast (パン酵母) / 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: 6.0 Å | ||||||||||||||||||
データ登録者 | Hung KYS / Klumpe S / Eisele MR / Elsasser S / Geng TT / Cheng TC / Joshi T / Rudack T / Sakata E / Finley D | ||||||||||||||||||
資金援助 | 米国, 5件
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引用 | ジャーナル: Nat Commun / 年: 2022 タイトル: Allosteric control of Ubp6 and the proteasome via a bidirectional switch. 著者: Ka Ying Sharon Hung / Sven Klumpe / Markus R Eisele / Suzanne Elsasser / Geng Tian / Shuangwu Sun / Jamie A Moroco / Tat Cheung Cheng / Tapan Joshi / Timo Seibel / Duco Van Dalen / Xin-Hua ...著者: Ka Ying Sharon Hung / Sven Klumpe / Markus R Eisele / Suzanne Elsasser / Geng Tian / Shuangwu Sun / Jamie A Moroco / Tat Cheung Cheng / Tapan Joshi / Timo Seibel / Duco Van Dalen / Xin-Hua Feng / Ying Lu / Huib Ovaa / John R Engen / Byung-Hoon Lee / Till Rudack / Eri Sakata / Daniel Finley / 要旨: The proteasome recognizes ubiquitinated proteins and can also edit ubiquitin marks, allowing substrates to be rejected based on ubiquitin chain topology. In yeast, editing is mediated by ...The proteasome recognizes ubiquitinated proteins and can also edit ubiquitin marks, allowing substrates to be rejected based on ubiquitin chain topology. In yeast, editing is mediated by deubiquitinating enzyme Ubp6. The proteasome activates Ubp6, whereas Ubp6 inhibits the proteasome through deubiquitination and a noncatalytic effect. Here, we report cryo-EM structures of the proteasome bound to Ubp6, based on which we identify mutants in Ubp6 and proteasome subunit Rpt1 that abrogate Ubp6 activation. The Ubp6 mutations define a conserved region that we term the ILR element. The ILR is found within the BL1 loop, which obstructs the catalytic groove in free Ubp6. Rpt1-ILR interaction opens the groove by rearranging not only BL1 but also a previously undescribed network of three interconnected active-site-blocking loops. Ubp6 activation and noncatalytic proteasome inhibition are linked in that they are eliminated by the same mutations. Ubp6 and ubiquitin together drive proteasomes into a unique conformation associated with proteasome inhibition. Thus, a multicomponent allosteric switch exerts simultaneous control over both Ubp6 and the proteasome. | ||||||||||||||||||
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_14084.map.gz | 180.7 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-14084-v30.xml emd-14084.xml | 57.9 KB 57.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_14084.png | 106.8 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-14084 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14084 | HTTPS FTP |
-関連構造データ
-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_14084.map.gz / 形式: CCP4 / 大きさ: 216 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 1.38 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
-試料の構成要素
+全体 : 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state
+超分子 #1: 26S proteasome Rpt1-RK -Ubp6-UbVS complex in the si state
+超分子 #2: yeast Rpt1-RK 26S proteasome in si state
+超分子 #3: Ubp6-UbVS complex
+分子 #1: Proteasome subunit alpha type-1
+分子 #2: Proteasome subunit alpha type-2
+分子 #3: Proteasome subunit alpha type-3
+分子 #4: Proteasome subunit alpha type-4
+分子 #5: Proteasome subunit alpha type-5
+分子 #6: Proteasome subunit alpha type-6
+分子 #7: Probable proteasome subunit alpha type-7
+分子 #8: Proteasome subunit beta type-1
+分子 #9: Proteasome subunit beta type-2
+分子 #10: Proteasome subunit beta type-3
+分子 #11: Proteasome subunit beta type-4
+分子 #12: Proteasome subunit beta type-5
+分子 #13: Proteasome subunit beta type-6
+分子 #14: Proteasome subunit beta type-7
+分子 #15: 26S proteasome regulatory subunit RPN10
+分子 #16: Ubiquitin carboxyl-terminal hydrolase RPN11
+分子 #17: 26S proteasome regulatory subunit RPN12
+分子 #18: 26S proteasome regulatory subunit RPN13
+分子 #19: 26S proteasome complex subunit SEM1
+分子 #20: 26S proteasome regulatory subunit RPN1
+分子 #21: 26S proteasome regulatory subunit RPN2
+分子 #22: 26S proteasome regulatory subunit RPN3
+分子 #23: 26S proteasome regulatory subunit RPN5
+分子 #24: 26S proteasome regulatory subunit RPN6
+分子 #25: 26S proteasome regulatory subunit RPN7
+分子 #26: 26S proteasome regulatory subunit RPN8
+分子 #27: 26S proteasome regulatory subunit RPN9
+分子 #28: 26S proteasome regulatory subunit 7 homolog
+分子 #29: 26S proteasome regulatory subunit 4 homolog
+分子 #30: 26S proteasome regulatory subunit 6B homolog
+分子 #31: 26S proteasome subunit RPT4
+分子 #32: 26S proteasome regulatory subunit 6A
+分子 #33: 26S proteasome regulatory subunit 8 homolog
+分子 #34: Ubiquitin carboxyl-terminal hydrolase 6
+分子 #35: Polyubiquitin-B
+分子 #36: ADENOSINE-5'-TRIPHOSPHATE
+分子 #37: MAGNESIUM ION
+分子 #38: 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
濃度 | 1.5 mg/mL |
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緩衝液 | pH: 7.4 |
グリッド | モデル: Quantifoil / 材質: COPPER / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
-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 / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 1.8 µm |
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: 35.0 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: MAXIMUM LIKELIHOOD |
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最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 6.0 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 64766 |