+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-24093 | |||||||||
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タイトル | Continuous movement of the pre-catalytic spliceosome, mode 2. | |||||||||
マップデータ | Continuous movement of the pre-catalytic spliceosome, mode 2. | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 Sm-like protein family complex / spliceosomal conformational changes to generate catalytic conformation / maturation of 5S rRNA / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / Lsm1-7-Pat1 complex / snoRNA guided rRNA 2'-O-methylation / U6 snRNP / box C/D sno(s)RNA 3'-end processing / positive regulation of RNA binding ...Sm-like protein family complex / spliceosomal conformational changes to generate catalytic conformation / maturation of 5S rRNA / mRNA decay by 5' to 3' exoribonuclease / snoRNA splicing / Lsm1-7-Pat1 complex / snoRNA guided rRNA 2'-O-methylation / U6 snRNP / box C/D sno(s)RNA 3'-end processing / positive regulation of RNA binding / generation of catalytic spliceosome for first transesterification step / deadenylation-dependent decapping of nuclear-transcribed mRNA / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / box C/D methylation guide snoRNP complex / splicing factor binding / U4/U6 snRNP / P-body assembly / 7-methylguanosine cap hypermethylation / pICln-Sm protein complex / spliceosomal tri-snRNP complex / small nuclear ribonucleoprotein complex / sno(s)RNA-containing ribonucleoprotein complex / U4 snRNA binding / SMN-Sm protein complex / mRNA cis splicing, via spliceosome / U2-type spliceosomal complex / U2-type prespliceosome assembly / U2-type catalytic step 2 spliceosome / commitment complex / U4 snRNP / U2 snRNP / poly(U) RNA binding / nuclear-transcribed mRNA catabolic process / U1 snRNP / U3 snoRNA binding / U2-type prespliceosome / tRNA processing / precatalytic spliceosome / spliceosomal complex assembly / generation of catalytic spliceosome for second transesterification step / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA 3'-splice site recognition / mRNA 5'-splice site recognition / spliceosomal tri-snRNP complex assembly / U5 snRNA binding / U5 snRNP / U2 snRNA binding / U6 snRNA binding / spliceosomal snRNP assembly / pre-mRNA intronic binding / maturation of SSU-rRNA / U1 snRNA binding / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / U4/U6 x U5 tri-snRNP complex / maturation of LSU-rRNA / catalytic step 2 spliceosome / small-subunit processome / P-body / spliceosomal complex / mRNA splicing, via spliceosome / rRNA processing / metallopeptidase activity / cytosolic large ribosomal subunit / RNA helicase activity / nucleic acid binding / ヘリカーゼ / response to xenobiotic stimulus / mRNA binding / GTPase activity / GTP binding / 核小体 / ATP hydrolysis activity / ミトコンドリア / RNA binding / zinc ion binding / 核質 / ATP binding / identical protein binding / metal ion binding / 細胞核 / 細胞質基質 / 細胞質 類似検索 - 分子機能 | |||||||||
生物種 | Saccharomyces cerevisiae (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: 20.0 Å | |||||||||
データ登録者 | Chen M / Ludtke SJ | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Nat Methods / 年: 2021 タイトル: Deep learning-based mixed-dimensional Gaussian mixture model for characterizing variability in cryo-EM. 著者: Muyuan Chen / Steven J Ludtke / 要旨: Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. Cryogenic electron microscopy (cryo-EM) provides direct visualization of individual ...Structural flexibility and/or dynamic interactions with other molecules is a critical aspect of protein function. Cryogenic electron microscopy (cryo-EM) provides direct visualization of individual macromolecules sampling different conformational and compositional states. While numerous methods are available for computational classification of discrete states, characterization of continuous conformational changes or large numbers of discrete state without human supervision remains challenging. Here we present e2gmm, a machine learning algorithm to determine a conformational landscape for proteins or complexes using a three-dimensional Gaussian mixture model mapped onto two-dimensional particle images in known orientations. Using a deep neural network architecture, e2gmm can automatically resolve the structural heterogeneity within the protein complex and map particles onto a small latent space describing conformational and compositional changes. This system presents a more intuitive and flexible representation than other manifold methods currently in use. We demonstrate this method on both simulated data and three biological systems to explore compositional and conformational changes at a range of scales. The software is distributed as part of EMAN2. | |||||||||
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_24093.map.gz | 7.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-24093-v30.xml emd-24093.xml | 19.1 KB 19.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_24093.png | 126.7 KB | ||
その他 | emd_24093_additional_1.map.gz emd_24093_additional_2.map.gz emd_24093_additional_3.map.gz emd_24093_additional_4.map.gz emd_24093_additional_5.map.gz | 7.3 MB 7.2 MB 7.5 MB 7.3 MB 7.3 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-24093 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24093 | HTTPS FTP |
-関連構造データ
関連構造データ | C: 同じ文献を引用 (文献) |
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類似構造データ |
-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_24093.map.gz / 形式: CCP4 / 大きさ: 8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Continuous movement of the pre-catalytic spliceosome, mode 2. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 4.2475 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
-追加マップ: Continuous movement of the pre-catalytic spliceosome, mode 2,...
ファイル | emd_24093_additional_1.map | ||||||||||||
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注釈 | Continuous movement of the pre-catalytic spliceosome, mode 2, frame 4. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Continuous movement of the pre-catalytic spliceosome, mode 2,...
ファイル | emd_24093_additional_2.map | ||||||||||||
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注釈 | Continuous movement of the pre-catalytic spliceosome, mode 2, frame 5. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Continuous movement of the pre-catalytic spliceosome, mode 2,...
ファイル | emd_24093_additional_3.map | ||||||||||||
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注釈 | Continuous movement of the pre-catalytic spliceosome, mode 2, frame 3. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Continuous movement of the pre-catalytic spliceosome, mode 2,...
ファイル | emd_24093_additional_4.map | ||||||||||||
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注釈 | Continuous movement of the pre-catalytic spliceosome, mode 2, frame 1. | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Continuous movement of the pre-catalytic spliceosome, mode 2,...
ファイル | emd_24093_additional_5.map | ||||||||||||
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注釈 | Continuous movement of the pre-catalytic spliceosome, mode 2, frame 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 : Pre-catalytic spliceosome
全体 | 名称: Pre-catalytic spliceosome |
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要素 |
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-超分子 #1: Pre-catalytic spliceosome
超分子 | 名称: Pre-catalytic spliceosome / タイプ: complex / ID: 1 / 親要素: 0 詳細: Re-processing of the dataset EMPIAR-10180 to resolve the continuous movement of the system. Five frames of the first motion mode are attached as additional map files. |
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由来(天然) | 生物種: Saccharomyces cerevisiae (パン酵母) |
-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
緩衝液 | pH: 8 |
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凍結 | 凍結剤: ETHANE |
詳細 | Re-processing of EMPIAR-10180. |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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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 FIELDBright-field microscopy |
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 56.0 e/Å2 |
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 EMDB ID: |
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初期 角度割当 | タイプ: NOT APPLICABLE |
最終 3次元分類 | ソフトウェア - 名称: EMAN (ver. 2.91) / 詳細: Deep learning based manifold embedding |
最終 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: EMAN (ver. 2.91) |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 20.0 Å / 解像度の算出法: OTHER / ソフトウェア - 名称: EMAN (ver. 2.91) 詳細: Each frame of the 3D structure of the continuous movement movie includes 4000 particles. The maps are filtered to 20A for visualization. 使用した粒子像数: 4000 |