+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-27018 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Human 19S-20S proteasome, state SD2 | |||||||||
マップデータ | ||||||||||
試料 |
| |||||||||
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 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / 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: 3.0 Å | |||||||||
データ登録者 | Zhao J | |||||||||
資金援助 | 1件
| |||||||||
引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2022 タイトル: Structural insights into the human PA28-20S proteasome enabled by efficient tagging and purification of endogenous proteins. 著者: Jianhua Zhao / Suraj Makhija / Chenyu Zhou / Hanxiao Zhang / YongQiang Wang / Monita Muralidharan / Bo Huang / Yifan Cheng / 要旨: The ability to produce folded and functional proteins is a necessity for structural biology and many other biological sciences. This task is particularly challenging for numerous biomedically ...The ability to produce folded and functional proteins is a necessity for structural biology and many other biological sciences. This task is particularly challenging for numerous biomedically important targets in human cells, including membrane proteins and large macromolecular assemblies, hampering mechanistic studies and drug development efforts. Here we describe a method combining CRISPR-Cas gene editing and fluorescence-activated cell sorting to rapidly tag and purify endogenous proteins in HEK cells for structural characterization. We applied this approach to study the human proteasome from HEK cells and rapidly determined cryogenic electron microscopy structures of major proteasomal complexes, including a high-resolution structure of intact human PA28αβ-20S. Our structures reveal that PA28 with a subunit stoichiometry of 3α/4β engages tightly with the 20S proteasome. Addition of a hydrophilic peptide shows that polypeptides entering through PA28 are held in the antechamber of 20S prior to degradation in the proteolytic chamber. This study provides critical insights into an important proteasome complex and demonstrates key methodologies for the tagging of proteins from endogenous sources. | |||||||||
履歴 |
|
-構造の表示
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_27018.map.gz | 16 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-27018-v30.xml emd-27018.xml | 50.4 KB 50.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_27018_fsc.xml | 20.8 KB | 表示 | FSCデータファイル |
画像 | emd_27018.png | 98.4 KB | ||
その他 | emd_27018_half_map_1.map.gz emd_27018_half_map_2.map.gz | 475.7 MB 475.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-27018 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27018 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_27018_validation.pdf.gz | 946.5 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_27018_full_validation.pdf.gz | 946.1 KB | 表示 | |
XML形式データ | emd_27018_validation.xml.gz | 26.2 KB | 表示 | |
CIF形式データ | emd_27018_validation.cif.gz | 33.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27018 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27018 | HTTPS FTP |
-関連構造データ
関連構造データ | 8cvtMC 7nanC 7naoC 7napC 7naqC 8cvrC 8cvsC 8cxbC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
---|---|
類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_27018.map.gz / 形式: CCP4 / 大きさ: 149.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ボクセルのサイズ | X=Y=Z: 1.06 Å | ||||||||||||||||||||
密度 |
| ||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
|
-添付データ
-ハーフマップ: #2
ファイル | emd_27018_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_27018_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
投影像・断面図 |
| ||||||||||||
密度ヒストグラム |
-試料の構成要素
+全体 : Human 19S-20S proteasome
+超分子 #1: Human 19S-20S proteasome
+分子 #1: 26S proteasome regulatory subunit 7
+分子 #2: 26S proteasome regulatory subunit 4
+分子 #3: 26S protease regulatory subunit 8
+分子 #4: 26S proteasome regulatory subunit 6B
+分子 #5: 26S protease regulatory subunit 10B
+分子 #6: 26S proteasome regulatory subunit 6A
+分子 #7: Proteasome subunit alpha type-6
+分子 #8: Proteasome subunit alpha type-2
+分子 #9: Proteasome subunit alpha type-4
+分子 #10: Proteasome subunit alpha type-7
+分子 #11: Proteasome subunit alpha type-5
+分子 #12: Proteasome subunit alpha type-1
+分子 #13: Proteasome subunit alpha type-3
+分子 #14: Proteasome subunit beta type-6
+分子 #15: Proteasome subunit beta type-7
+分子 #16: Proteasome subunit beta type-3
+分子 #17: Proteasome subunit beta type-2
+分子 #18: Proteasome subunit beta type-5
+分子 #19: Proteasome subunit beta type-1
+分子 #20: Proteasome subunit beta type-4
+分子 #21: 26S proteasome non-ATPase regulatory subunit 1
+分子 #22: 26S proteasome non-ATPase regulatory subunit 3
+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 7
+分子 #27: 26S proteasome non-ATPase regulatory subunit 13
+分子 #28: 26S proteasome non-ATPase regulatory subunit 4
+分子 #29: 26S proteasome non-ATPase regulatory subunit 14
+分子 #30: 26S proteasome non-ATPase regulatory subunit 8
+分子 #31: 26S proteasome complex subunit SEM1
+分子 #32: 26S proteasome non-ATPase regulatory subunit 2
+分子 #33: ADENOSINE-5'-TRIPHOSPHATE
+分子 #34: N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-y...
+分子 #35: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.5 |
---|---|
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 30.0 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 / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 1.0 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |