+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4v8t | ||||||||||||
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タイトル | Cryo-EM Structure of the 60S Ribosomal Subunit in Complex with Arx1 and Rei1 | ||||||||||||
要素 |
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キーワード | RIBOSOME / LARGE RIBOSOMAL SUBUNIT / RIBOSOME BIOGENESIS / RIBOSOME MATURATION FACTOR | ||||||||||||
機能・相同性 | 機能・相同性情報 加水分解酵素 / hexon binding / 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 / protein kinase activator activity / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) ...加水分解酵素 / hexon binding / 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 / protein kinase activator activity / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of a pool of free 40S subunits / negative regulation of mRNA splicing, via spliceosome / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / translational elongation / ribosomal large subunit export from nucleus / 90S preribosome / regulation of translational fidelity / protein-RNA complex assembly / ribonucleoprotein complex binding / translational termination / Neutrophil degranulation / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / translational initiation / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / metallopeptidase activity / ribosome biogenesis / viral capsid / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / 5S rRNA binding / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / host cell nucleus / nucleolus / proteolysis / RNA binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||||||||
生物種 | Saccharomyces cerevisiae S288C (パン酵母) SACCHAROMYCES CEREVISIAE (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: 8.1 Å | ||||||||||||
データ登録者 | Greber, B.J. / Boehringer, D. / Montellese, C. / Ban, N. | ||||||||||||
引用 | ジャーナル: Nat Struct Mol Biol / 年: 2012 タイトル: Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit. 著者: Basil J Greber / Daniel Boehringer / Christian Montellese / Nenad Ban / 要旨: Eukaryotic ribosome biogenesis requires many protein factors that facilitate the assembly, nuclear export and final maturation of 40S and 60S particles. We have biochemically characterized ribosomal ...Eukaryotic ribosome biogenesis requires many protein factors that facilitate the assembly, nuclear export and final maturation of 40S and 60S particles. We have biochemically characterized ribosomal complexes of the yeast 60S-biogenesis factor Arx1 and late-maturation factors Rei1 and Jjj1 and determined their cryo-EM structures. Arx1 was visualized bound to the 60S subunit together with Rei1, at 8.1-Å resolution, to reveal the molecular details of Arx1 binding whereby Arx1 arrests the eukaryotic-specific rRNA expansion segment 27 near the polypeptide tunnel exit. Rei1 and Jjj1, which have been implicated in Arx1 recycling, bind in the vicinity of Arx1 and form a network of interactions. We suggest that, in addition to the role of Arx1 during pre-60S nuclear export, the binding of Arx1 conformationally locks the pre-60S subunit and inhibits the premature association of nascent chain-processing factors to the polypeptide tunnel exit. | ||||||||||||
履歴 |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "VB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "fA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-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 | 4v8t.cif.gz | 3.2 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4v8t.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 4v8t.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
文書・要旨 | 4v8t_validation.pdf.gz | 1.3 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4v8t_full_validation.pdf.gz | 1.9 MB | 表示 | |
XML形式データ | 4v8t_validation.xml.gz | 263.3 KB | 表示 | |
CIF形式データ | 4v8t_validation.cif.gz | 433.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/v8/4v8t ftp://data.pdbj.org/pub/pdb/validation_reports/v8/4v8t | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
+60S ribosomal protein ... , 40種, 40分子 ABCDEFGHIJKLMNPQRSTUVWXYZabcde...
-Large ribosomal subunit protein ... , 2種, 2分子 Oq
#15: タンパク質 | 分子量: 22247.227 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae S288C (パン酵母) 株: S288C / 参照: UniProt: P26784 |
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#43: 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) 株: S288C / 参照: UniProt: P05317 |
-タンパク質 , 2種, 2分子 mt
#39: 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) 株: S288C / 参照: UniProt: P0CH08 |
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#46: タンパク質 | 分子量: 67848.047 Da / 分子数: 1 / 由来タイプ: 組換発現 / 詳細: N-TERMINAL HIS-TAG 由来: (組換発現) Saccharomyces cerevisiae S288C (パン酵母) 株: S288C / 遺伝子: ARX1, YDR101C, YD8557.10c / プラスミド: PPROEX-HTB / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / Variant (発現宿主): Rosetta / 参照: UniProt: Q03862, 加水分解酵素 |
-RIBOSOMAL PROTEIN ... , 2種, 2分子 rs
#44: タンパク質 | 分子量: 14912.779 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母), (天然) Saccharomyces cerevisiae S288C (パン酵母) 株: S288C / 参照: UniProt: P05318 |
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#45: タンパク質・ペプチド | 分子量: 3932.839 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: S288C |
-RNA鎖 , 4種, 4分子 1578
#47: RNA鎖 | 分子量: 36810.594 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) SACCHAROMYCES CEREVISIAE (パン酵母) / 株: S288C |
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#48: RNA鎖 | 分子量: 1097493.875 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Saccharomyces cerevisiae S288C (パン酵母) 株: S288C / 参照: GenBank: 834774822 |
#49: 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) 株: S288C / 参照: GenBank: 834774822 |
#50: 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) 株: S288C / 参照: GenBank: 940534893 |
-非ポリマー , 1種, 4分子
#51: 化合物 | ChemComp-ZN / |
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-詳細
配列の詳細 | (1) THESE ARE PARTS OF THE PROTEIN SEQUENCES MODELED AS UNK RESIDUES. (2) THE MICROHETEROGENEITY ...(1) THESE ARE PARTS OF THE PROTEIN SEQUENCES MODELED AS UNK RESIDUES. (2) THE MICROHETER |
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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: 60S RIBOSOMAL SUBUNIT IN COMPLEX WITH ARX1 AND REI1 / タイプ: RIBOSOME |
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緩衝液 | 名称: 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2 pH: 8 詳細: 20 MM HEPES-NAOH PH 8.0, 50 MM NACL, 5 MM BETA- MERCAPTOETHANOL, 5 MM MGCL2 |
試料 | 濃度: 0.16 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 詳細: PLUNGE FREEZING IN LIQUID ETHANE AFTER MANUAL BLOTTING USING A MANUAL PLUNGE FREEZING DEVICE |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI TECNAI 20 / 日付: 2012年2月21日 |
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電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 83000 X / 最大 デフォーカス(公称値): 4500 nm / 最小 デフォーカス(公称値): 1500 nm / Cs: 2.3 mm |
試料ホルダ | 温度: 87 K / 傾斜角・最大: 0 ° |
撮影 | 電子線照射量: 20 e/Å2 フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: PER FRAME | |||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||||||||
3次元再構成 | 手法: PROJECTION MATCHING / 解像度: 8.1 Å / 粒子像の数: 84113 / ピクセルサイズ(公称値): 1.81 Å 詳細: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2169. (DEPOSITION ID: 10977). 対称性のタイプ: POINT | |||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: REAL / Target criteria: Cross-correlation coefficient / 詳細: METHOD--RIGID BODY REFINEMENT PROTOCOL--RIGID BODY | |||||||||||||||||||||
原子モデル構築 |
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精密化 | 最高解像度: 8.1 Å | |||||||||||||||||||||
精密化ステップ | サイクル: LAST / 最高解像度: 8.1 Å
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