+
データを開く
-
基本情報
登録情報 | データベース: EMDB / ID: EMD-3227 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM map of a native 80S-ribosome-eIF-5A complex | |||||||||
![]() | Ribosome reconstruction | |||||||||
![]() |
| |||||||||
![]() | Translation | |||||||||
機能・相同性 | ![]() positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / positive regulation of translational termination / positive regulation of translational elongation / 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) / response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane ...positive regulation of cytoplasmic translational elongation through polyproline stretches / Hypusine synthesis from eIF5A-lysine / CAT tailing / translational frameshifting / positive regulation of translational termination / positive regulation of translational elongation / 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) / 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 / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / regulation of translational fidelity / positive regulation of translational initiation / protein-RNA complex assembly / translation elongation factor activity / translational termination / translation initiation factor activity / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translational initiation / macroautophagy / maintenance of translational fidelity / ribosomal large subunit assembly / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / ribosome binding / 5S rRNA binding / large ribosomal subunit rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / perinuclear region of cytoplasm / mitochondrion / RNA binding / nucleus / metal ion binding / cytoplasm / cytosol 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.88 Å | |||||||||
![]() | Schmidt C / Becker T / Heuer A / Braunger K / Shanmuganathan V / Pech M / m Berninghausen O / Wilson D / Beckmann R | |||||||||
![]() | ![]() タイトル: Structure of the hypusinylated eukaryotic translation factor eIF-5A bound to the ribosome. 著者: Christian Schmidt / Thomas Becker / André Heuer / Katharina Braunger / Vivekanandan Shanmuganathan / Markus Pech / Otto Berninghausen / Daniel N Wilson / Roland Beckmann / ![]() 要旨: During protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5A (a/eIF-5A) and in bacteria by the ...During protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5A (a/eIF-5A) and in bacteria by the homologous protein EF-P. While a structure of EF-P bound to the 70S ribosome exists, structural insight into eIF-5A on the 80S ribosome has been lacking. Here we present a cryo-electron microscopy reconstruction of eIF-5A bound to the yeast 80S ribosome at 3.9 Å resolution. The structure reveals that the unique and functionally essential post-translational hypusine modification reaches toward the peptidyltransferase center of the ribosome, where the hypusine moiety contacts A76 of the CCA-end of the P-site tRNA. These findings would support a model whereby eIF-5A stimulates peptide bond formation on polyproline-stalled ribosomes by stabilizing and orienting the CCA-end of the P-tRNA, rather than by directly contributing to the catalysis. | |||||||||
履歴 |
|
-
構造の表示
ムービー |
![]() |
---|---|
構造ビューア | EMマップ: ![]() ![]() ![]() |
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 | ![]() | 179.3 MB | ![]() | |
---|---|---|---|---|
ヘッダ (付随情報) | ![]() ![]() | 9.9 KB 9.9 KB | 表示 表示 | ![]() |
画像 | ![]() | 160.5 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 325.7 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 324.8 KB | 表示 | |
XML形式データ | ![]() | 6.8 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
-
リンク
EMDBのページ | ![]() ![]() |
---|---|
「今月の分子」の関連する項目 |
-
マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Ribosome reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.084 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-
試料の構成要素
-全体 : Native 80S ribosome-eIF-5A complex from yeast
全体 | 名称: Native 80S ribosome-eIF-5A complex from yeast |
---|---|
要素 |
|
-超分子 #1000: Native 80S ribosome-eIF-5A complex from yeast
超分子 | 名称: Native 80S ribosome-eIF-5A complex from yeast / タイプ: sample / ID: 1000 / 詳細: Sample was obtained from a native pullout / 集合状態: One ribosome binds one eIF-5A molecule / Number unique components: 2 |
---|
-超分子 #1: Ribosome
超分子 | 名称: Ribosome / タイプ: complex / ID: 1 / 組換発現: No / Ribosome-details: ribosome-eukaryote: ALL |
---|---|
由来(天然) | 生物種: ![]() ![]() |
-分子 #1: eIF-5A
分子 | 名称: eIF-5A / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 集合状態: monomer / 組換発現: No |
---|---|
由来(天然) | 生物種: ![]() ![]() |
分子量 | 理論値: 170 KDa |
配列 | UniProtKB: Eukaryotic translation initiation factor 5A-1 |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
![]() | 単粒子再構成法 |
試料の集合状態 | particle |
-
試料調製
緩衝液 | pH: 7.4 詳細: 20 mM HEPES, pH7.4, 100 mM KOAc, 10 mM MgCl2, 0.01 mg/ml Cycloheximide |
---|---|
グリッド | 詳細: Quantifoil R3/3 grids with 2 nM carbon on top |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK IV |
-
電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
日付 | 2015年2月25日 |
撮影 | カテゴリ: CCD フィルム・検出器のモデル: FEI FALCON II (4k x 4k) 実像数: 3786 詳細: The data was provided with the semi-automated software EPU (FEI Company) with a dose of 2.4 electrons per frame for 13 frames in total. The frames were aligned with the Motion Correction software ビット/ピクセル: 16 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 3.4 µm / 最小 デフォーカス(公称値): 0.8 µm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
-
画像解析
詳細 | Computational sorting and classification was done in SPIDER, movie processing and high resolution refinement was done with RELION |
---|---|
CTF補正 | 詳細: Each Particle |
最終 再構成 | 想定した対称性 - 点群: C1 (非対称) / アルゴリズム: OTHER / 解像度のタイプ: BY AUTHOR / 解像度: 3.88 Å / 解像度の算出法: OTHER ソフトウェア - 名称: SIGNATURE, CTFFIND3, SPIDER, RELION 使用した粒子像数: 62532 |