+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-0202 | |||||||||
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タイトル | Cryo-EM structure of the ribosome-NatA complex | |||||||||
マップデータ | Ribosome-NatA complex aligned on the ribosome and filtered according to local resolution. | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 N-terminal protein amino acid propionylation / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal methionine Nalpha-acetyltransferase NatE / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) ...N-terminal protein amino acid propionylation / peptide-glutamate-alpha-N-acetyltransferase activity / N-terminal amino-acid Nalpha-acetyltransferase NatA / N-terminal methionine Nalpha-acetyltransferase NatE / peptide-serine-alpha-N-acetyltransferase activity / NatA complex / N-terminal protein amino acid acetylation / peptide alpha-N-acetyltransferase activity / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / mitotic sister chromatid cohesion / response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / protein-RNA complex assembly / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / regulation of translational fidelity / translational termination / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maintenance of translational fidelity / オートファジー / modification-dependent protein catabolic process / protein tag activity / ribosomal large subunit assembly / rRNA processing / large ribosomal subunit rRNA binding / ribosome binding / リボソーム生合成 / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / protein ubiquitination / リボソーム / structural constituent of ribosome / 翻訳 (生物学) / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / ミトコンドリア / RNA 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: 3.4 Å | |||||||||
データ登録者 | Knorr AG / Becker T / Berninghausen O / Beckmann R | |||||||||
資金援助 | ドイツ, 2件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2019 タイトル: Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation. 著者: Alexandra G Knorr / Christian Schmidt / Petr Tesina / Otto Berninghausen / Thomas Becker / Birgitta Beatrix / Roland Beckmann / 要旨: The majority of eukaryotic proteins are N-terminally α-acetylated by N-terminal acetyltransferases (NATs). Acetylation usually occurs co-translationally and defects have severe consequences. ...The majority of eukaryotic proteins are N-terminally α-acetylated by N-terminal acetyltransferases (NATs). Acetylation usually occurs co-translationally and defects have severe consequences. Nevertheless, it is unclear how these enzymes act in concert with the translating ribosome. Here, we report the structure of a native ribosome-NatA complex from Saccharomyces cerevisiae. NatA (comprising Naa10, Naa15 and Naa50) displays a unique mode of ribosome interaction by contacting eukaryotic-specific ribosomal RNA expansion segments in three out of four binding patches. Thereby, NatA is dynamically positioned directly underneath the ribosomal exit tunnel to facilitate modification of the emerging nascent peptide chain. Methionine amino peptidases, but not chaperones or signal recognition particle, would be able to bind concomitantly. This work assigns a function to the hitherto enigmatic ribosomal RNA expansion segments and provides mechanistic insights into co-translational protein maturation by N-terminal acetylation. | |||||||||
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_0202.map.gz | 162.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-0202-v30.xml emd-0202.xml | 70.9 KB 70.9 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_0202.png | 192.9 KB | ||
その他 | emd_0202_additional.map.gz | 264.8 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-0202 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0202 | 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_0202.map.gz / 形式: CCP4 / 大きさ: 282.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Ribosome-NatA complex aligned on the ribosome and filtered according to local resolution. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.084 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: Ribosome-NatA complex aligned on the ribosome, postprocessed unfiltered...
ファイル | emd_0202_additional.map | ||||||||||||
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注釈 | Ribosome-NatA complex aligned on the ribosome, postprocessed unfiltered map. | ||||||||||||
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 : Ribosome-NatA complex
+超分子 #1: Ribosome-NatA complex
+超分子 #2: 60S ribosomal subunit
+超分子 #3: N-terminal acetyl transferase A
+分子 #1: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), m...
+分子 #2: 5S rRNA
+分子 #3: 5.8S rRNA
+分子 #4: tRNA
+分子 #5: P-site tRNA
+分子 #6: 60S ribosomal protein L42-A
+分子 #7: 60S ribosomal protein L43-A
+分子 #8: 60S ribosomal protein L2-A
+分子 #9: 60S ribosomal protein L3
+分子 #10: 60S ribosomal protein L4-A
+分子 #11: 60S ribosomal protein L5
+分子 #12: 60S ribosomal protein L6-A
+分子 #13: 60S ribosomal protein L7-A
+分子 #14: 60S ribosomal protein L8-A
+分子 #15: 60S ribosomal protein L9-A
+分子 #16: 60S ribosomal protein L11-A
+分子 #17: 60S ribosomal protein L13-A
+分子 #18: 60S ribosomal protein L14-A
+分子 #19: 60S ribosomal protein L15-A
+分子 #20: 60S ribosomal protein L16-A
+分子 #21: 60S ribosomal protein L17-A
+分子 #22: 60S ribosomal protein L18-A
+分子 #23: 60S ribosomal protein L19-A
+分子 #24: 60S ribosomal protein L20-A
+分子 #25: 60S ribosomal protein L21-A
+分子 #26: 60S ribosomal protein L22-A
+分子 #27: 60S ribosomal protein L23-A
+分子 #28: 60S ribosomal protein L24-A
+分子 #29: 60S ribosomal protein L25
+分子 #30: 60S ribosomal protein L26-A
+分子 #31: 60S ribosomal protein L27-A
+分子 #32: 60S ribosomal protein L28
+分子 #33: 60S ribosomal protein L29
+分子 #34: 60S ribosomal protein L30
+分子 #35: 60S ribosomal protein L31-A
+分子 #36: 60S ribosomal protein L32
+分子 #37: 60S ribosomal protein L33-A
+分子 #38: 60S ribosomal protein L34-A
+分子 #39: 60S ribosomal protein L35-A
+分子 #40: 60S ribosomal protein L36-A
+分子 #41: 60S ribosomal protein L37-A
+分子 #42: 60S ribosomal protein L38
+分子 #43: 60S ribosomal protein L39
+分子 #44: Ubiquitin-60S ribosomal protein L40
+分子 #45: 60S ribosomal protein L41-A
+分子 #46: ribosomal protein RPL1
+分子 #47: 60S ribosomal protein L10
+分子 #48: N-terminal acetyltransferase A complex subunit NAT1
+分子 #49: N-terminal acetyltransferase A complex catalytic subunit ARD1
+分子 #50: N-alpha-acetyltransferase NAT5
+分子 #51: nascent polypeptide chain
+分子 #52: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
-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: 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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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: FEI FALCON II (4k x 4k) 平均電子線量: 2.5 e/Å2 |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
-画像解析
CTF補正 | ソフトウェア - 名称: Gctf |
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初期 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION |
最終 角度割当 | タイプ: PROJECTION MATCHING / ソフトウェア - 名称: RELION |
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / ソフトウェア - 名称: RELION (ver. 2.1) / 使用した粒子像数: 262507 |
-原子モデル構築 1
精密化 | プロトコル: RIGID BODY FIT |
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得られたモデル | PDB-6hd7: |