+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 5apn | ||||||
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タイトル | Structure of the yeast 60S ribosomal subunit in complex with Arx1, Alb1 and N-terminally tagged Rei1 | ||||||
要素 |
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キーワード | RIBOSOME (リボソーム) / EUKARYOTIC RIBOSOME BIOGENESIS / RIBOSOME MATURATION / RIBOSOME BIOGENESIS FACTOR / 60S RIBOSOMAL SUBUNIT (リボソーム) / REI1 / ARX1 / ALB1 / CRYO-EM (低温電子顕微鏡法) / RIBOSOMAL POLYPEPTIDE EXIT TUNNEL PROOFREADING | ||||||
機能・相同性 | 機能・相同性情報 budding cell bud growth / 加水分解酵素 / nucleocytoplasmic transport / 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 / 90S preribosome / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits ...budding cell bud growth / 加水分解酵素 / nucleocytoplasmic transport / 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 / 90S preribosome / 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 / Neutrophil degranulation / maintenance of translational fidelity / オートファジー / modification-dependent protein catabolic process / ribosomal large subunit assembly / protein tag activity / rRNA processing / metallopeptidase activity / large ribosomal subunit rRNA binding / リボソーム生合成 / mitotic cell cycle / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / negative regulation of translation / sequence-specific DNA binding / 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 / 核小体 / タンパク質分解 / RNA binding / zinc ion binding / 核質 / 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 S288c (パン酵母) Saccharomyces cerevisiae S288C (パン酵母) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.91 Å | ||||||
データ登録者 | Greber, B.J. / Gerhardy, S. / Leitner, A. / Leibundgut, M. / Salem, M. / Boehringer, D. / Leulliot, N. / Aebersold, R. / Panse, V.G. / Ban, V. | ||||||
引用 | ジャーナル: Cell / 年: 2016 タイトル: Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation. 著者: Basil Johannes Greber / Stefan Gerhardy / Alexander Leitner / Marc Leibundgut / Michèle Salem / Daniel Boehringer / Nicolas Leulliot / Ruedi Aebersold / Vikram Govind Panse / Nenad Ban / 要旨: Eukaryotic ribosome biogenesis depends on several hundred assembly factors to produce functional 40S and 60S ribosomal subunits. The final phase of 60S subunit biogenesis is cytoplasmic maturation, ...Eukaryotic ribosome biogenesis depends on several hundred assembly factors to produce functional 40S and 60S ribosomal subunits. The final phase of 60S subunit biogenesis is cytoplasmic maturation, which includes the proofreading of functional centers of the 60S subunit and the release of several ribosome biogenesis factors. We report the cryo-electron microscopy (cryo-EM) structure of the yeast 60S subunit in complex with the biogenesis factors Rei1, Arx1, and Alb1 at 3.4 Å resolution. In addition to the network of interactions formed by Alb1, the structure reveals a mechanism for ensuring the integrity of the ribosomal polypeptide exit tunnel. Arx1 probes the entire set of inner-ring proteins surrounding the tunnel exit, and the C terminus of Rei1 is deeply inserted into the ribosomal tunnel, where it forms specific contacts along almost its entire length. We provide genetic and biochemical evidence that failure to insert the C terminus of Rei1 precludes subsequent steps of 60S maturation. | ||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 5apn.cif.gz | 3.2 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb5apn.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 5apn.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ap/5apn ftp://data.pdbj.org/pub/pdb/validation_reports/ap/5apn | HTTPS FTP |
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-関連構造データ
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
-RNA鎖 , 3種, 3分子 578
#1: RNA鎖 | 分子量: 1094369.625 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae S288c (パン酵母) 参照: GenBank: 329138943 |
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#2: RNA鎖 | 分子量: 38951.105 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae S288c (パン酵母) 参照: GenBank: 329138943 |
#3: RNA鎖 | 分子量: 50682.922 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae S288c (パン酵母) 参照: GenBank: 329138943 |
+60S ribosomal protein ... , 39種, 39分子 ABCDEFGHIJLMNOPQRSTUVWXYZabcde...
-タンパク質 , 5種, 5分子 mqxyz
#41: タンパク質 | 分子量: 14583.077 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae S288c (パン酵母) 参照: UniProt: P0CH08 |
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#44: タンパク質 | 分子量: 33749.121 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae S288c (パン酵母) 参照: UniProt: P05317 |
#45: タンパク質 | 分子量: 67835.188 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Saccharomyces cerevisiae S288c (パン酵母) 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): ROSETTA 2 / 参照: UniProt: Q03862, 加水分解酵素 |
#46: タンパク質 | 分子量: 48492.180 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Saccharomyces cerevisiae S288c (パン酵母) プラスミド: PPROEX-HTB / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): ROSETTA 2 / 参照: UniProt: P38344 |
#47: タンパク質 | 分子量: 7251.930 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母) 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): ROSETTA 2 |
-非ポリマー , 2種, 286分子
#48: 化合物 | ChemComp-MG / #49: 化合物 | ChemComp-ZN / |
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-詳細
配列の詳細 | The correct register of the chain z remains unknown for some parts of the model. Hence they are ...The correct register of the chain z remains unknown for some parts of the model. Hence they are built in as UNK. However, the sample sequence for chain z corresponds to UniProt P47019.1 |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: YEAST 60S ARX1 ALB1 6XHIS-REI1 / タイプ: RIBOSOME 詳細: QUANTIFOIL HOLEY CARBON GRIDS WERE COATED WITH A THIN CARBON FILM |
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緩衝液 | 名称: 20MM / pH: 8 / 詳細: 20MM |
試料 | 濃度: 0.2 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: HOLEY CARBON |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE-PROPANE / 詳細: PLUNGE-FROZEN |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS / 日付: 2015年4月17日 / 詳細: COLLECTED IN MOVIE MODE |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 59000 X / 倍率(補正後): 100720 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm |
試料ホルダ | 温度: 80 K |
撮影 | 電子線照射量: 20 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
画像スキャン | デジタル画像の数: 670 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: PER DETECTOR FRAME | ||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||
3次元再構成 | 手法: MAXIMUM LIKELIHOOD BASED REFINEMENT IMPLEMENTED IN RELION 解像度: 3.91 Å / 粒子像の数: 22040 / ピクセルサイズ(実測値): 1.39 Å 詳細: FOR VISUALIZATION PURPOSES THE FINAL MAP WAS FILTERED AND AMPLITUDE CORRECTED IN RELION. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3152 (DEPOSITION ID 13746). THE COORDINATES WERE ...詳細: FOR VISUALIZATION PURPOSES THE FINAL MAP WAS FILTERED AND AMPLITUDE CORRECTED IN RELION. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3152 (DEPOSITION ID 13746). THE COORDINATES WERE REFINED IN RECIPROCAL SPACE USING PHENIX.REFINE AGAINST THE MLHL TARGET. FOR THIS, THE CRYO-EM MAP WAS CONVERTED TO RECIPROCAL SPACE STRUCTURE FACTORS. 対称性のタイプ: POINT | ||||||||||||||||||||
原子モデル構築 | 空間: REAL |