+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-6693 | |||||||||||||||||||||
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タイトル | the resting state of yeast proteasome | |||||||||||||||||||||
マップデータ | ||||||||||||||||||||||
試料 |
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キーワード | resting state yeast proteasome nucleotide occupied / HYDROLASE | |||||||||||||||||||||
機能・相同性 | 機能・相同性情報 SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome ...SAGA complex localization to transcription regulatory region / Metalloprotease DUBs / peroxisome fission / proteasome storage granule assembly / transcription export complex 2 / proteasome regulatory particle assembly / protein deneddylation / maintenance of DNA trinucleotide repeats / filamentous growth / COP9 signalosome / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / protein-containing complex localization / proteasome-activating activity / mitochondrial fission / proteasome regulatory particle, base subcomplex / metal-dependent deubiquitinase activity / nonfunctional rRNA decay / K48-linked polyubiquitin modification-dependent protein binding / 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 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / peptide catabolic process / KEAP1-NFE2L2 pathway / proteasome binding / CDK-mediated phosphorylation and removal of Cdc6 / Neddylation / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / regulation of protein catabolic process / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / polyubiquitin modification-dependent protein binding / endopeptidase activator activity / protein deubiquitination / 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 / Ub-specific processing proteases / threonine-type endopeptidase activity / mRNA export from nucleus / enzyme regulator activity / ERAD pathway / protein folding chaperone / Neutrophil degranulation / proteasome complex / ubiquitin binding / nucleotide-excision repair / positive regulation of transcription elongation by RNA polymerase II / double-strand break repair via homologous recombination / positive regulation of protein catabolic process / metallopeptidase activity / peroxisome / protein-macromolecule adaptor activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / endopeptidase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / molecular adaptor activity / regulation of cell cycle / chromatin remodeling / protein domain specific binding / mRNA binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||||||||||||||
生物種 | Saccharomyces cerevisiae (パン酵母) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (パン酵母) | |||||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.3 Å | |||||||||||||||||||||
データ登録者 | Ding Z / Cong Y | |||||||||||||||||||||
資金援助 | 中国, 6件
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引用 | ジャーナル: Cell Res / 年: 2017 タイトル: High-resolution cryo-EM structure of the proteasome in complex with ADP-AlFx. 著者: Zhanyu Ding / Zhenglin Fu / Cong Xu / Yifan Wang / Yanxing Wang / Junrui Li / Liangliang Kong / Jinhuan Chen / Na Li / Rongguang Zhang / Yao Cong / 要旨: The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic- ...The 26S proteasome is an ATP-dependent dynamic 2.5 MDa protease that regulates numerous essential cellular functions through degradation of ubiquitinated substrates. Here we present a near-atomic-resolution cryo-EM map of the S. cerevisiae 26S proteasome in complex with ADP-AlFx. Our biochemical and structural data reveal that the proteasome-ADP-AlFx is in an activated state, displaying a distinct conformational configuration especially in the AAA-ATPase motor region. Noteworthy, this map demonstrates an asymmetric nucleotide binding pattern with four consecutive AAA-ATPase subunits bound with nucleotide. The remaining two subunits, Rpt2 and Rpt6, with empty or only partially occupied nucleotide pocket exhibit pronounced conformational changes in the AAA-ATPase ring, which may represent a collective result of allosteric cooperativity of all the AAA-ATPase subunits responding to ATP hydrolysis. This collective motion of Rpt2 and Rpt6 results in an elevation of their pore loops, which could play an important role in substrate processing of proteasome. Our data also imply that the nucleotide occupancy pattern could be related to the activation status of the complex. Moreover, the HbYX tail insertion may not be sufficient to maintain the gate opening of 20S core particle. Our results provide new insights into the mechanisms of nucleotide-driven allosteric cooperativity of the complex and of the substrate processing by 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_6693.map.gz | 10.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-6693-v30.xml emd-6693.xml | 52.2 KB 52.2 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_6693.png | 51.2 KB | ||
Filedesc metadata | emd-6693.cif.gz | 13.3 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-6693 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6693 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_6693_validation.pdf.gz | 386.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_6693_full_validation.pdf.gz | 386.4 KB | 表示 | |
XML形式データ | emd_6693_validation.xml.gz | 7.2 KB | 表示 | |
CIF形式データ | emd_6693_validation.cif.gz | 8.3 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6693 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6693 | 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_6693.map.gz / 形式: CCP4 / 大きさ: 178 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: 1.318 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 : The yeast resting state proteasome
+超分子 #1: The yeast resting state proteasome
+分子 #1: 26S protease regulatory subunit 4 homolog
+分子 #2: 26S protease regulatory subunit 6B homolog
+分子 #3: Proteasome subunit beta type-2
+分子 #4: Proteasome subunit alpha type-1
+分子 #5: Proteasome subunit beta type-3
+分子 #6: Probable proteasome subunit alpha type-7
+分子 #7: Proteasome subunit alpha type-6
+分子 #8: Proteasome subunit alpha type-5
+分子 #9: Proteasome subunit alpha type-4
+分子 #10: 26S proteasome complex subunit SEM1
+分子 #11: 26S proteasome regulatory subunit RPN2
+分子 #12: 26S proteasome regulatory subunit RPN3
+分子 #13: 26S proteasome regulatory subunit RPN12
+分子 #14: 26S proteasome regulatory subunit RPN7
+分子 #15: 26S proteasome regulatory subunit RPN6
+分子 #16: 26S protease regulatory subunit 8 homolog
+分子 #17: 26S protease subunit RPT4
+分子 #18: 26S protease regulatory subunit 6A
+分子 #19: 26S proteasome regulatory subunit RPN8
+分子 #20: 26S proteasome regulatory subunit RPN10
+分子 #21: 26S proteasome regulatory subunit RPN9
+分子 #22: 26S proteasome regulatory subunit RPN5
+分子 #23: 26S protease regulatory subunit 7 homolog
+分子 #24: Proteasome subunit alpha type-3
+分子 #25: Proteasome subunit alpha type-2
+分子 #26: Proteasome subunit beta type-1
+分子 #27: Proteasome subunit beta type-4
+分子 #28: Proteasome subunit beta type-5
+分子 #29: Proteasome subunit beta type-6
+分子 #30: Proteasome subunit beta type-7
+分子 #31: 26S proteasome regulatory subunit RPN13
+分子 #32: 26S proteasome regulatory subunit RPN1
+分子 #33: Ubiquitin carboxyl-terminal hydrolase RPN11
-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 | cell |
-試料調製
緩衝液 | pH: 7.5 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 平均電子線量: 25.0 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 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
初期モデル | モデルのタイプ: EMDB MAP |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 6.3 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 26000 |
初期 角度割当 | タイプ: PROJECTION MATCHING |
最終 角度割当 | タイプ: PROJECTION MATCHING |