+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-9512 | ||||||||||||
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タイトル | Cryo-EM map of the human 26S proteasome at 3.5A resolution with C2 symmetry | ||||||||||||
マップデータ | with C2 symmetry | ||||||||||||
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 / integrator complex / proteasome accessory complex / purine ribonucleoside triphosphate binding / meiosis I ...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 / integrator complex / proteasome accessory complex / purine ribonucleoside triphosphate binding / meiosis I / positive regulation of proteasomal protein catabolic process / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / metal-dependent deubiquitinase activity / protein K63-linked deubiquitination / proteasome regulatory particle, base subcomplex / regulation of endopeptidase activity / negative regulation of programmed cell death / 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 / proteasome core complex / Regulation of ornithine decarboxylase (ODC) / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / K63-linked deubiquitinase activity / Impaired BRCA2 binding to RAD51 / 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 / general transcription initiation factor binding / NF-kappaB binding / endopeptidase activator activity / proteasome assembly / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / polyubiquitin modification-dependent protein binding / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / positive regulation of RNA polymerase II transcription preinitiation complex assembly / mRNA export from nucleus / regulation of proteasomal protein catabolic process / enzyme regulator activity / ERAD pathway / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / inclusion body / negative regulation of inflammatory response to antigenic stimulus / : / sarcomere / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / ciliary basal body / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / proteolysis involved in protein catabolic process / 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 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / stem cell differentiation / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / lipopolysaccharide binding / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / double-strand break repair via homologous recombination / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / P-body / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 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: 3.5 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_9512.map.gz | 478.8 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-9512-v30.xml emd-9512.xml | 50.5 KB 50.5 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_9512.png | 32.5 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-9512 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9512 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_9512_validation.pdf.gz | 531 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_9512_full_validation.pdf.gz | 530.6 KB | 表示 | |
XML形式データ | emd_9512_validation.xml.gz | 7.8 KB | 表示 | |
CIF形式データ | emd_9512_validation.cif.gz | 9 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9512 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9512 | 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_9512.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 | with C2 symmetry | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.07 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
+超分子 #1: human 26S proteasome
+分子 #1: 26S protease regulatory subunit 4
+分子 #2: 26S protease regulatory subunit 7
+分子 #3: 26S protease regulatory subunit 10B
+分子 #4: 26S protease regulatory subunit 6A
+分子 #5: 26S protease regulatory subunit 8
+分子 #6: 26S protease regulatory subunit 6B
+分子 #7: 26S proteasome non-ATPase regulatory subunit 1
+分子 #8: 26S proteasome non-ATPase regulatory subunit 13
+分子 #9: 26S proteasome non-ATPase regulatory subunit 12
+分子 #10: 26S proteasome non-ATPase regulatory subunit 11
+分子 #11: 26S proteasome non-ATPase regulatory subunit 6
+分子 #12: 26S proteasome non-ATPase regulatory subunit 3
+分子 #13: 26S proteasome non-ATPase regulatory subunit 8
+分子 #14: 26S proteasome non-ATPase regulatory subunit 7
+分子 #15: 26S proteasome non-ATPase regulatory subunit 14
+分子 #16: 26S proteasome non-ATPase regulatory subunit 4
+分子 #17: 26S proteasome complex subunit DSS1
+分子 #18: 26S proteasome non-ATPase regulatory subunit 2
+分子 #19: Proteasome subunit alpha type-6
+分子 #20: Proteasome subunit alpha type-2
+分子 #21: Proteasome subunit alpha type-4
+分子 #22: Proteasome subunit alpha type-7
+分子 #23: Proteasome subunit alpha type-5
+分子 #24: Proteasome subunit alpha type-1
+分子 #25: Proteasome subunit alpha type-3
+分子 #26: Proteasome subunit beta type-6
+分子 #27: Proteasome subunit beta type-7
+分子 #28: Proteasome subunit beta type-3
+分子 #29: Proteasome subunit beta type-2
+分子 #30: Proteasome subunit beta type-5
+分子 #31: Proteasome subunit beta type-1
+分子 #32: Proteasome subunit beta type-4
+分子 #33: 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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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 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 最大 デフォーカス(補正後): 0.0026 µm / 最小 デフォーカス(補正後): 0.0016 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |