+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4v4b | |||||||||
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タイトル | Structure of the ribosomal 80S-eEF2-sordarin complex from yeast obtained by docking atomic models for RNA and protein components into a 11.7 A cryo-EM map. | |||||||||
要素 |
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キーワード | RIBOSOME (リボソーム) / 80S ribosome / 40S ribosomal subunit (リボソーム) / eEF2 / tRNA translocation / sordarin / cryo-EM (低温電子顕微鏡法) | |||||||||
機能・相同性 | 機能・相同性情報 Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / ヒドロキシル化 / : / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / positive regulation of translational elongation / Protein methylation / RMTs methylate histone arginines / positive regulation of translational fidelity / ヒドロキシル化 / : / Formation of the ternary complex, and subsequently, the 43S complex / Translation initiation complex formation / Ribosomal scanning and start codon recognition / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / preribosome, small subunit precursor / translational elongation / response to cycloheximide / Major pathway of rRNA processing in the nucleolus and cytosol / 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 / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit export from nucleus / preribosome, large subunit precursor / L13a-mediated translational silencing of Ceruloplasmin expression / ribosomal large subunit export from nucleus / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / regulation of translational fidelity / translation elongation factor activity / translational termination / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / DNA-(apurinic or apyrimidinic site) endonuclease activity / Neutrophil degranulation / small-subunit processome / maintenance of translational fidelity / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / ribosomal small subunit biogenesis / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / ribosomal small subunit assembly / rRNA processing / cytoplasmic stress granule / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / ribosome binding / large ribosomal subunit / small ribosomal subunit / cytoplasmic translation / 5S rRNA binding / cytosolic large ribosomal subunit / protein-folding chaperone binding / negative regulation of translation / rRNA binding / リボソーム / structural constituent of ribosome / 翻訳 (生物学) / ribonucleoprotein complex / response to antibiotic / mRNA binding / GTPase activity / GTP binding / 核小体 / ミトコンドリア / RNA binding / zinc ion binding / 核質 / 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 | 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: 11.7 Å | |||||||||
データ登録者 | Spahn, C.M. / Gomez-Lorenzo, M.G. / Grassucci, R.A. / Jorgensen, R. / Andersen, G.R. / Beckmann, R. / Penczek, P.A. / Ballesta, J.P.G. / Frank, J. | |||||||||
引用 | ジャーナル: EMBO J / 年: 2004 タイトル: Domain movements of elongation factor eEF2 and the eukaryotic 80S ribosome facilitate tRNA translocation. 著者: Christian M T Spahn / Maria G Gomez-Lorenzo / Robert A Grassucci / Rene Jørgensen / Gregers R Andersen / Roland Beckmann / Pawel A Penczek / Juan P G Ballesta / Joachim Frank / 要旨: An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and ...An 11.7-A-resolution cryo-EM map of the yeast 80S.eEF2 complex in the presence of the antibiotic sordarin was interpreted in molecular terms, revealing large conformational changes within eEF2 and the 80S ribosome, including a rearrangement of the functionally important ribosomal intersubunit bridges. Sordarin positions domain III of eEF2 so that it can interact with the sarcin-ricin loop of 25S rRNA and protein rpS23 (S12p). This particular conformation explains the inhibitory action of sordarin and suggests that eEF2 is stalled on the 80S ribosome in a conformation that has similarities with the GTPase activation state. A ratchet-like subunit rearrangement (RSR) occurs in the 80S.eEF2.sordarin complex that, in contrast to Escherichia coli 70S ribosomes, is also present in vacant 80S ribosomes. A model is suggested, according to which the RSR is part of a mechanism for moving the tRNAs during the translocation reaction. #1: ジャーナル: Nat Struct Biol / 年: 1999 タイトル: EF-G-dependent GTP hydrolysis induces translocation accompanied by large conformational changes in the 70S ribosome. 著者: R K Agrawal / A B Heagle / P Penczek / R A Grassucci / J Frank / 要旨: Cryo-electron microscopy has been used to visualize elongation factor G (EF-G) on the 70S ribosome in GDP and GTP states. GTP hydrolysis is required for binding of all the domains of EF-G to the ...Cryo-electron microscopy has been used to visualize elongation factor G (EF-G) on the 70S ribosome in GDP and GTP states. GTP hydrolysis is required for binding of all the domains of EF-G to the pretranslocational complex and for the completion of translocation. In addition, large conformational changes have been identified in the ribosome. The head of the 30S subunit shifts toward the L1 protein side, and the L7/L12 stalk becomes bifurcated upon EF-G binding. Upon GTP hydrolysis, the bifurcation is reversed and an arc-like connection is formed between the base of the stalk and EF-G. #2: ジャーナル: PROG.NUCLEIC ACID RES.MOL.BIOL. / 年: 1996 タイトル: The large ribosomal subunit stalk as a regulatory element of the eukaryotic translational machinery. 著者: Ballesta, J.P. / Remacha, M. #3: ジャーナル: Science / 年: 2000 タイトル: The complete atomic structure of the large ribosomal subunit at 2.4 A resolution 著者: Ban, N. / Nissen, P. / Hansen, J. / Moore, P.B. / Steitz, T.A. | |||||||||
履歴 |
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Remark 400 | COMPOUND PDB ENTRIES 1S1H AND 1S1I REPRESENT ONE CRYO-EM STRUCTURE OF THE SACCHAROMYCES CEREVISIAE ...COMPOUND PDB ENTRIES 1S1H AND 1S1I REPRESENT ONE CRYO-EM STRUCTURE OF THE SACCHAROMYCES CEREVISIAE 80S RIBOSOME. THIS FILE, 1S1H, CONTAINS THE 40S SUBUNIT. THE 60S RIBOSOMAL SUBUNIT IS IN FILE 1S1I. |
-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 | 4v4b.cif.gz | 3.6 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4v4b.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 4v4b.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/v4/4v4b ftp://data.pdbj.org/pub/pdb/validation_reports/v4/4v4b | 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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-要素
-RNA鎖 , 3種, 3分子 AAB3B4
#1: RNA鎖 | 分子量: 489331.719 Da / 分子数: 1 / 由来タイプ: 天然 詳細: modelled as analogous molecule of T. thermophilus taken from PDB entry 1FJF 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 155076 |
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#18: RNA鎖 | 分子量: 971012.312 Da / 分子数: 1 / 由来タイプ: 天然 詳細: REPRESENTED BY THE ANALOGOUS MOLECULE OF H. MARISMORTUI TAKEN FROM PDB ENTRY 1FFK AND SUPPLEMENTED WITH SEQUENCES FROM PDB ENTRIES 1MMS, 1MZP AND 1GIY 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 3377778 |
#19: RNA鎖 | 分子量: 40298.008 Da / 分子数: 1 / 由来タイプ: 天然 詳細: REPRESENTED BY THE ANALOGOUS MOLECULE OF H. MARISMORTUI TAKEN FROM PDB ENTRY 1FFK 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: GenBank: 3377779 |
-タンパク質 , 1種, 1分子 AT
#2: タンパク質 | 分子量: 93407.125 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P32324 |
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-40S ribosomal protein ... , 15種, 15分子 ABACADAEAGAHAIAJAKALAMANAOAQAS
#3: タンパク質 | 分子量: 20355.412 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P32905 |
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#4: タンパク質 | 分子量: 21321.918 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05750 |
#5: タンパク質 | 分子量: 20363.400 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: O13516 |
#6: タンパク質 | 分子量: 15639.166 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P25443 |
#7: タンパク質 | 分子量: 16577.156 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P26783 |
#8: タンパク質 | 分子量: 14518.867 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P04648, UniProt: Q3E7Y3*PLUS |
#9: タンパク質 | 分子量: 15746.292 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P40213, UniProt: P0CX52*PLUS |
#10: タンパク質 | 分子量: 11352.213 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P38701 |
#11: タンパク質 | 分子量: 14459.474 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P06367 |
#12: タンパク質 | 分子量: 12879.160 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P32827, UniProt: P0CX30*PLUS |
#13: タンパク質 | 分子量: 15485.841 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P35271, UniProt: P0CX56*PLUS |
#14: タンパク質・ペプチド | 分子量: 4328.041 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P41058 |
#15: タンパク質 | 分子量: 7841.351 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P05756 |
#16: タンパク質 | 分子量: 8777.438 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: P26781, UniProt: P0CX48*PLUS |
#17: タンパク質 | 分子量: 8901.519 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Saccharomyces cerevisiae (パン酵母) / 参照: UniProt: Q01855 |
+60S ribosomal protein ... , 28種, 28分子 BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVB0BWBXBYBZB9
-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 |
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