+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9511 | ||||||||||||
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タイトル | Cryo-EM map of the human 26S proteasome bound to USP14_UbAl | ||||||||||||
マップデータ | Human 26S proteasome bound to USP14-UbAl | ||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 negative regulation of ERAD pathway / 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 / deubiquitinase activity / 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 / regulation of chemotaxis ...negative regulation of ERAD pathway / 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 / deubiquitinase activity / 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 / regulation of chemotaxis / 減数分裂 / purine ribonucleoside triphosphate binding / positive regulation of proteasomal protein catabolic process / metal-dependent deubiquitinase activity / proteasome regulatory particle / 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 / hypothalamus gonadotrophin-releasing hormone neuron development / 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 / female meiosis I / Regulation of ornithine decarboxylase (ODC) / proteasome core complex / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / positive regulation of protein monoubiquitination / mitochondrion transport along microtubule / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / fat pad development / Somitogenesis / K63-linked deubiquitinase activity / Impaired BRCA2 binding to RAD51 / endopeptidase inhibitor activity / immune system process / myofibril / female gonad development / proteasome binding / seminiferous tubule development / regulation of protein catabolic process / protein deubiquitination / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / 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 / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / enzyme regulator activity / mRNA export from nucleus / energy homeostasis / regulation of neuron apoptotic process / : / 封入体 / regulation of proteasomal protein catabolic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / Maturation of protein E / negative regulation of ubiquitin-dependent protein catabolic process / Maturation of protein E / ER Quality Control Compartment (ERQC) / negative regulation of inflammatory response to antigenic stimulus / 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 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Endosomal Sorting Complex Required For Transport (ESCRT) / NOTCH2 Activation and Transmission of Signal to the Nucleus / 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 / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / response to organonitrogen compound / 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 類似検索 - 分子機能 | ||||||||||||
生物種 | Homo sapiens (ヒト) / Human (ヒト) | ||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 4.35 Å | ||||||||||||
データ登録者 | Huang XL / Luan B / Wu JP / Shi YG | ||||||||||||
資金援助 | 中国, 3件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2016 タイトル: An atomic structure of the human 26S proteasome. 著者: Xiuliang Huang / Bai Luan / Jianping Wu / Yigong Shi / 要旨: We report the cryo-EM structure of the human 26S proteasome at an average resolution of 3.5 Å, allowing atomic modeling of 28 subunits in the core particle (CP) and 18 subunits in the regulatory ...We report the cryo-EM structure of the human 26S proteasome at an average resolution of 3.5 Å, allowing atomic modeling of 28 subunits in the core particle (CP) and 18 subunits in the regulatory particle (RP). The C-terminal residues of Rpt3 and Rpt5 subunits in the RP can be seen inserted into surface pockets formed between adjacent α subunits in the CP. Each of the six Rpt subunits contains a bound nucleotide, and the central gate of the CP α-ring is closed despite RP association. The six pore 1 loops in the Rpt ring are arranged similarly to a spiral staircase along the axial channel of substrate transport, which is constricted by the pore 2 loops. We also determined the cryo-EM structure of the human proteasome bound to the deubiquitinating enzyme USP14 at 4.35-Å resolution. Together, our structures provide a framework for mechanistic understanding of eukaryotic proteasome function. | ||||||||||||
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_9511.map.gz | 480 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9511-v30.xml emd-9511.xml | 52.7 KB 52.7 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_9511.png | 45.1 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9511 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9511 | 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_9511.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Human 26S proteasome bound to USP14-UbAl | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.07 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 : human 26S proteasome bound to USP14-UbAl
+超分子 #1: human 26S proteasome bound to USP14-UbAl
+分子 #1: Proteasome subunit beta type-6
+分子 #2: Proteasome subunit alpha type-6
+分子 #3: Proteasome subunit beta type-7
+分子 #4: Proteasome subunit alpha type-2
+分子 #5: Proteasome subunit beta type-3
+分子 #6: Proteasome subunit alpha type-4
+分子 #7: Proteasome subunit beta type-2
+分子 #8: Proteasome subunit alpha type-7
+分子 #9: Proteasome subunit beta type-5
+分子 #10: Proteasome subunit alpha type-5
+分子 #11: Proteasome subunit beta type-1
+分子 #12: Proteasome subunit alpha type-1
+分子 #13: Proteasome subunit beta type-4
+分子 #14: 26S protease regulatory subunit 7
+分子 #15: 26S protease regulatory subunit 4
+分子 #16: 26S protease regulatory subunit 8
+分子 #17: 26S protease regulatory subunit 6B
+分子 #18: 26S protease regulatory subunit 10B
+分子 #19: 26S protease regulatory subunit 6A
+分子 #20: 26S proteasome non-ATPase regulatory subunit 1
+分子 #21: Proteasome subunit alpha type-3
+分子 #22: 26S proteasome non-ATPase regulatory subunit 13
+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 3
+分子 #27: 26S proteasome non-ATPase regulatory subunit 8
+分子 #28: 26S proteasome non-ATPase regulatory subunit 7
+分子 #29: 26S proteasome non-ATPase regulatory subunit 14
+分子 #30: 26S proteasome non-ATPase regulatory subunit 4
+分子 #31: 26S proteasome complex subunit DSS1
+分子 #32: 26S proteasome non-ATPase regulatory subunit 2
+分子 #33: Ubiquitin carboxyl-terminal hydrolase 14
+分子 #34: Polyubiquitin-B
+分子 #35: 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 mg/mL | ||||||||||||
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緩衝液 | pH: 8 構成要素:
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グリッド | 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 3.0 nm / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 雰囲気: AIR | ||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 281 K / 装置: FEI VITROBOT MARK IV / 詳細: blot for 2 seconds before plunging. | ||||||||||||
詳細 | This sample was monodisperse. |
-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 / Cs: 2.7 mm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
温度 | 最低: 70.0 K |
詳細 | Preliminary grid screening was performed manually |
撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) デジタル化 - サイズ - 横: 4096 pixel / デジタル化 - サイズ - 縦: 4096 pixel / デジタル化 - 画像ごとのフレーム数: 1-26 / 平均露光時間: 1.6 sec. / 平均電子線量: 37.0 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
粒子像選択 | 選択した数: 534096 |
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CTF補正 | ソフトウェア - 名称: CTFFIND (ver. 3) |
初期モデル | モデルのタイプ: EMDB MAP EMDB ID: |
初期 角度割当 | タイプ: ANGULAR RECONSTITUTION / ソフトウェア - 名称: RELION (ver. 1.4) |
最終 3次元分類 | クラス数: 5 / ソフトウェア - 名称: RELION (ver. 1.4) |
最終 角度割当 | タイプ: ANGULAR RECONSTITUTION / ソフトウェア - 名称: RELION (ver. 1.4) |
最終 再構成 | 使用したクラス数: 1 / 解像度のタイプ: BY AUTHOR / 解像度: 4.35 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 1.4) / 使用した粒子像数: 141293 |