+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10586 | |||||||||
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タイトル | Rat 20S proteasome | |||||||||
マップデータ | endogenous rat liver 20S proteasome, local resolution filtered | |||||||||
試料 |
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キーワード | PROTEASOME / HYDROLASE | |||||||||
機能・相同性 | 機能・相同性情報 Cross-presentation of soluble exogenous antigens (endosomes) / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of ornithine decarboxylase (ODC) / Assembly of the pre-replicative complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A ...Cross-presentation of soluble exogenous antigens (endosomes) / SCF-beta-TrCP mediated degradation of Emi1 / Regulation of ornithine decarboxylase (ODC) / Assembly of the pre-replicative complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / UCH proteinases / CDK-mediated phosphorylation and removal of Cdc6 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / The role of GTSE1 in G2/M progression after G2 checkpoint / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX3 expression and activity / GLI3 is processed to GLI3R by the proteasome / Activation of NF-kappaB in B cells / Degradation of beta-catenin by the destruction complex / Degradation of AXIN / Regulation of RAS by GAPs / Orc1 removal from chromatin / Neddylation / AUF1 (hnRNP D0) binds and destabilizes mRNA / MAPK6/MAPK4 signaling / Regulation of PTEN stability and activity / KEAP1-NFE2L2 pathway / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / ABC-family proteins mediated transport / Ub-specific processing proteases / proteasome core complex / Neutrophil degranulation / immune system process / myofibril / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / negative regulation of inflammatory response to antigenic stimulus / : / sarcomere / proteasome complex / ciliary basal body / proteolysis involved in protein catabolic process / lipopolysaccharide binding / P-body / response to virus / response to organic cyclic compound / nuclear matrix / peptidase activity / positive regulation of NF-kappaB transcription factor activity / postsynapse / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / response to oxidative stress / ribosome / centrosome / ubiquitin protein ligase binding / synapse / proteolysis / RNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | Rattus norvegicus (ドブネズミ) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.7 Å | |||||||||
データ登録者 | Deshmukh FK / Polkinghorn CR | |||||||||
資金援助 | イスラエル, 2件
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引用 | ジャーナル: ACS Cent Sci / 年: 2020 タイトル: Comparative Structural Analysis of 20S Proteasome Ortholog Protein Complexes by Native Mass Spectrometry. 著者: Shay Vimer / Gili Ben-Nissan / David Morgenstern / Fanindra Kumar-Deshmukh / Caley Polkinghorn / Royston S Quintyn / Yury V Vasil'ev / Joseph S Beckman / Nadav Elad / Vicki H Wysocki / Michal Sharon / 要旨: Ortholog protein complexes are responsible for equivalent functions in different organisms. However, during evolution, each organism adapts to meet its physiological needs and the environmental ...Ortholog protein complexes are responsible for equivalent functions in different organisms. However, during evolution, each organism adapts to meet its physiological needs and the environmental challenges imposed by its niche. This selection pressure leads to structural diversity in protein complexes, which are often difficult to specify, especially in the absence of high-resolution structures. Here, we describe a multilevel experimental approach based on native mass spectrometry (MS) tools for elucidating the structural preservation and variations among highly related protein complexes. The 20S proteasome, an essential protein degradation machinery, served as our model system, wherein we examined five complexes isolated from different organisms. We show that throughout evolution, from the archaeal prokaryotic complex to the eukaryotic 20S proteasomes in yeast () and mammals (rat - , rabbit - and human - HEK293 cells), the proteasome increased both in size and stability. Native MS structural signatures of the rat and rabbit 20S proteasomes, which heretofore lacked high-resolution, three-dimensional structures, highly resembled that of the human complex. Using cryoelectron microscopy single-particle analysis, we were able to obtain a high-resolution structure of the rat 20S proteasome, allowing us to validate the MS-based results. Our study also revealed that the yeast complex, and not those in mammals, was the largest in size and displayed the greatest degree of kinetic stability. Moreover, we also identified a new proteoform of the PSMA7 subunit that resides within the rat and rabbit complexes, which to our knowledge have not been previously described. Altogether, our strategy enables elucidation of the unique structural properties of protein complexes that are highly similar to one another, a framework that is valid not only to ortholog protein complexes, but also for other highly related protein assemblies. | |||||||||
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_10586.map.gz | 146.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-10586-v30.xml emd-10586.xml | 32.5 KB 32.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_10586_fsc.xml | 14.2 KB | 表示 | FSCデータファイル |
画像 | emd_10586.png | 203.6 KB | ||
マスクデータ | emd_10586_msk_1.map | 244.1 MB | マスクマップ | |
Filedesc metadata | emd-10586.cif.gz | 8.4 KB | ||
その他 | emd_10586_half_map_1.map.gz emd_10586_half_map_2.map.gz | 192.3 MB 192.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10586 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10586 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_10586_validation.pdf.gz | 462.7 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_10586_full_validation.pdf.gz | 461.9 KB | 表示 | |
XML形式データ | emd_10586_validation.xml.gz | 20 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10586 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10586 | 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_10586.map.gz / 形式: CCP4 / 大きさ: 244.1 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | endogenous rat liver 20S proteasome, local resolution filtered | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.86 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
-マスク #1
ファイル | emd_10586_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Rat 20S proteasome, Unfiltered half map 2
ファイル | emd_10586_half_map_1.map | ||||||||||||
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注釈 | Rat 20S proteasome, Unfiltered half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Rat 20S proteasome, Unfiltered half map 1
ファイル | emd_10586_half_map_2.map | ||||||||||||
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注釈 | Rat 20S proteasome, Unfiltered half map 1 | ||||||||||||
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 : Rat liver 20S proteasome
+超分子 #1: Rat liver 20S proteasome
+分子 #1: Proteasome subunit alpha type-6
+分子 #2: Proteasome subunit alpha type-2
+分子 #3: Proteasome subunit alpha type-4
+分子 #4: Proteasome subunit alpha type-7
+分子 #5: Proteasome subunit alpha type-5
+分子 #6: Proteasome subunit alpha type-1
+分子 #7: Proteasome subunit alpha type-3
+分子 #8: Proteasome subunit beta type-6
+分子 #9: Proteasome subunit beta type-7
+分子 #10: Proteasome subunit beta type-3
+分子 #11: Proteasome subunit beta type-2
+分子 #12: Proteasome subunit beta type-5
+分子 #13: Proteasome subunit beta type-1
+分子 #14: Proteasome subunit beta type-4
-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 | 14 mg/mL |
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緩衝液 | pH: 7.4 / 構成要素 - 濃度: 160.0 mM / 構成要素 - 式: K3PO4 / 構成要素 - 名称: Potassium phosphate |
グリッド | モデル: C-flat-2/2 / 材質: COPPER / メッシュ: 300 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 60 sec. / 前処理 - 雰囲気: AIR / 前処理 - 気圧: 0.052000000000000005 kPa 詳細: Grids were glow discharged 30 minutes before applying the sample. |
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 / 詳細: blot for 3 seconds. |
詳細 | Purified endogenous rat liver 20S proteasome |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 20 eV |
詳細 | Preliminary grid screening was performed on Talos Arctica |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 / 実像数: 2234 / 平均露光時間: 1.5 sec. / 平均電子線量: 37.0 e/Å2 詳細: Images were collected in movie-mode at 45 frames per second |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | C2レンズ絞り径: 70.0 µm / 照射モード: OTHER / 撮影モード: DIFFRACTION / Cs: 2.7 mm / 最大 デフォーカス(公称値): 1.6 µm / 最小 デフォーカス(公称値): 0.6 µm / 倍率(公称値): 105000 |
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 |
+画像解析
-原子モデル構築 1
精密化 | プロトコル: FLEXIBLE FIT |
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得られたモデル | PDB-6tu3: |