+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-23028 | |||||||||||||||||||||
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タイトル | Negative stain EM structure of the human SAGA coactivator complex (TRRAP, core, splicing module) | |||||||||||||||||||||
マップデータ | map | |||||||||||||||||||||
試料 |
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キーワード | splicing / gene regulation / transcription / chromatin | |||||||||||||||||||||
機能・相同性 | 機能・相同性情報 SAGA-type complex / regulation of primary metabolic process / regulation of somatic stem cell population maintenance / regulation of cellular response to stress / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / transcription factor TFTC complex / SLIK (SAGA-like) complex / hepatocyte differentiation ...SAGA-type complex / regulation of primary metabolic process / regulation of somatic stem cell population maintenance / regulation of cellular response to stress / SAGA complex assembly / lateral mesodermal cell differentiation / allantois development / transcription factor TFTC complex / SLIK (SAGA-like) complex / hepatocyte differentiation / splicing factor binding / negative regulation of microtubule depolymerization / U12-type spliceosomal complex / maintenance of protein location in nucleus / RNA splicing, via transesterification reactions / U2-type precatalytic spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / RNA polymerase binding / limb development / SAGA complex / U2 snRNP / transcription preinitiation complex / transcription factor TFIID complex / precatalytic spliceosome / RNA polymerase II general transcription initiation factor activity / negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / nucleus organization / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / mRNA Splicing - Minor Pathway / regulation of RNA splicing / histone deacetylase complex / histone acetyltransferase complex / embryonic placenta development / positive regulation of transcription initiation by RNA polymerase II / U2 snRNA binding / somitogenesis / regulation of DNA repair / RNA polymerase II preinitiation complex assembly / gastrulation / RNA Polymerase II Pre-transcription Events / visual perception / TBP-class protein binding / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / RNA splicing / male germ cell nucleus / DNA-templated transcription initiation / promoter-specific chromatin binding / nuclear estrogen receptor binding / transcription initiation at RNA polymerase II promoter / transcription coregulator activity / spliceosomal complex / mRNA transcription by RNA polymerase II / multicellular organism growth / negative regulation of protein catabolic process / autophagy / nuclear matrix / microtubule cytoskeleton organization / mRNA splicing, via spliceosome / cytoplasmic ribonucleoprotein granule / G1/S transition of mitotic cell cycle / transcription corepressor activity / microtubule cytoskeleton / HATs acetylate histones / positive regulation of cell growth / DNA-binding transcription factor binding / Regulation of TP53 Activity through Phosphorylation / transcription by RNA polymerase II / transcription coactivator activity / protein stabilization / Ub-specific processing proteases / nuclear speck / chromatin remodeling / protein heterodimerization activity / focal adhesion / apoptotic process / protein-containing complex binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of apoptotic process / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / enzyme binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus 類似検索 - 分子機能 | |||||||||||||||||||||
生物種 | Homo sapiens (ヒト) / unclassified Rhodococcus (バクテリア) | |||||||||||||||||||||
手法 | 単粒子再構成法 / ネガティブ染色法 / 解像度: 19.09 Å | |||||||||||||||||||||
データ登録者 | Herbst DA / Esbin MN | |||||||||||||||||||||
資金援助 | 米国, European Union, スイス, 6件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2021 タイトル: Structure of the human SAGA coactivator complex. 著者: Dominik A Herbst / Meagan N Esbin / Robert K Louder / Claire Dugast-Darzacq / Gina M Dailey / Qianglin Fang / Xavier Darzacq / Robert Tjian / Eva Nogales / 要旨: The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are ...The SAGA complex is a regulatory hub involved in gene regulation, chromatin modification, DNA damage repair and signaling. While structures of yeast SAGA (ySAGA) have been reported, there are noteworthy functional and compositional differences for this complex in metazoans. Here we present the cryogenic-electron microscopy (cryo-EM) structure of human SAGA (hSAGA) and show how the arrangement of distinct structural elements results in a globally divergent organization from that of yeast, with a different interface tethering the core module to the TRRAP subunit, resulting in a dramatically altered geometry of functional elements and with the integration of a metazoan-specific splicing module. Our hSAGA structure reveals the presence of an inositol hexakisphosphate (InsP) binding site in TRRAP and an unusual property of its pseudo-(Ψ)PIKK. Finally, we map human disease mutations, thus providing the needed framework for structure-guided drug design of this important therapeutic target for human developmental diseases and cancer. | |||||||||||||||||||||
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_23028.map.gz | 94.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-23028-v30.xml emd-23028.xml | 47.5 KB 47.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_23028_fsc.xml | 10.8 KB | 表示 | FSCデータファイル |
画像 | emd_23028.png | 74.3 KB | ||
マスクデータ | emd_23028_msk_1.map | 103 MB | マスクマップ | |
Filedesc metadata | emd-23028.cif.gz | 13.3 KB | ||
その他 | emd_23028_half_map_1.map.gz emd_23028_half_map_2.map.gz | 80.8 MB 80.6 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-23028 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23028 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_23028_validation.pdf.gz | 860.4 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_23028_full_validation.pdf.gz | 859.9 KB | 表示 | |
XML形式データ | emd_23028_validation.xml.gz | 17 KB | 表示 | |
CIF形式データ | emd_23028_validation.cif.gz | 22.5 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23028 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23028 | 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_23028.map.gz / 形式: CCP4 / 大きさ: 103 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.4 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_23028_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: half map 1
ファイル | emd_23028_half_map_1.map | ||||||||||||
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注釈 | half map 1 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: half map 2
ファイル | emd_23028_half_map_2.map | ||||||||||||
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注釈 | half map 2 | ||||||||||||
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 : human SAGA
+超分子 #1: human SAGA
+超分子 #2: human SAGA
+超分子 #3: STAGA complex 65 subunit gamma
+分子 #1: Transformation/transcription domain-associated protein,Transforma...
+分子 #2: TAF5-like RNA polymerase II p300/CBP-associated factor-associated...
+分子 #3: Isoform 3 of Transcription factor SPT20 homolog
+分子 #4: STAGA complex 65 subunit gamma, DhaA,STAGA complex 65 subunit gam...
+分子 #5: Transcription initiation factor TFIID subunit 9B
+分子 #6: TAF6-like RNA polymerase II p300/CBP-associated factor-associated...
+分子 #7: Transcription initiation factor TFIID subunit 12
+分子 #8: Transcription initiation factor TFIID subunit 10
+分子 #9: Transcription initiation protein SPT3 homolog,Transcription initi...
+分子 #10: Transcriptional adapter 1
+分子 #11: Ataxin-7
+分子 #12: Splicing factor 3B subunit 3
+分子 #13: Splicing factor 3B subunit 5
-実験情報
-構造解析
手法 | ネガティブ染色法 |
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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
緩衝液 | pH: 7.5 構成要素:
詳細: Buffers were freshly prepared and 0.22 um filtered. | ||||||||||||||||||
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染色 | タイプ: NEGATIVE / 材質: uranyl formate | ||||||||||||||||||
グリッド | モデル: Homemade / 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. / 前処理 - 雰囲気: AIR / 前処理 - 気圧: 101.325 kPa | ||||||||||||||||||
詳細 | The sample was crosslinked with 1 mM bis(sulfosuccinimidyl)suberate (BS3) prior to freezing |
-電子顕微鏡法
顕微鏡 | FEI TECNAI 20 |
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撮影 | フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) 撮影したグリッド数: 1 / 実像数: 745 / 平均電子線量: 35.0 e/Å2 |
電子線 | 加速電圧: 120 kV / 電子線源: FIELD EMISSION GUN |
電子光学系 | 照射モード: SPOT SCAN / 撮影モード: BRIGHT FIELD / Cs: 2.2 mm / 最大 デフォーカス(公称値): 3.9 µm / 最小 デフォーカス(公称値): 0.4 µm / 倍率(公称値): 80000 |
試料ステージ | 試料ホルダーモデル: SIDE ENTRY, EUCENTRIC |
+画像解析
-原子モデル構築 1
初期モデル |
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精密化 | 空間: REAL / プロトコル: RIGID BODY FIT | ||||||
得られたモデル | PDB-7kts: |