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データを開く
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基本情報
登録情報 | ![]() | |||||||||
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タイトル | CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME : PARENTAL STRAIN | |||||||||
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![]() | CRYO-EM LEISHMANIA MAJOR 80S RIBOSOME WILD TYPE / RIBOSOME | |||||||||
機能・相同性 | ![]() ciliary transition zone / ciliary plasm / nuclear lumen / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / protein-RNA complex assembly / maturation of LSU-rRNA / translation regulator activity / rescue of stalled ribosome ...ciliary transition zone / ciliary plasm / nuclear lumen / negative regulation of translational frameshifting / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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) / protein-RNA complex assembly / maturation of LSU-rRNA / translation regulator activity / rescue of stalled ribosome / protein kinase C binding / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / small-subunit processome / modification-dependent protein catabolic process / protein tag activity / maintenance of translational fidelity / rRNA processing / kinase activity / ribosome biogenesis / ribosome binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / protein ubiquitination / negative regulation of translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / nucleus / cytosol / cytoplasm 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: 2.4 Å | |||||||||
![]() | Rajan KS / Yonath A | |||||||||
資金援助 | European Union, 1件
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![]() | ![]() タイトル: Structural and mechanistic insights into the function of Leishmania ribosome lacking a single pseudouridine modification. 著者: K Shanmugha Rajan / Saurav Aryal / Disha-Gajanan Hiregange / Anat Bashan / Hava Madmoni / Mika Olami / Tirza Doniger / Smadar Cohen-Chalamish / Pascal Pescher / Masato Taoka / Yuko Nobe / ...著者: K Shanmugha Rajan / Saurav Aryal / Disha-Gajanan Hiregange / Anat Bashan / Hava Madmoni / Mika Olami / Tirza Doniger / Smadar Cohen-Chalamish / Pascal Pescher / Masato Taoka / Yuko Nobe / Aliza Fedorenko / Tanaya Bose / Ella Zimermann / Eric Prina / Noa Aharon-Hefetz / Yitzhak Pilpel / Toshiaki Isobe / Ron Unger / Gerald F Späth / Ada Yonath / Shulamit Michaeli / ![]() ![]() ![]() 要旨: Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the ...Leishmania is the causative agent of cutaneous and visceral diseases affecting millions of individuals worldwide. Pseudouridine (Ψ), the most abundant modification on rRNA, changes during the parasite life cycle. Alterations in the level of a specific Ψ in helix 69 (H69) affected ribosome function. To decipher the molecular mechanism of this phenotype, we determine the structure of ribosomes lacking the single Ψ and its parental strain at ∼2.4-3 Å resolution using cryo-EM. Our findings demonstrate the significance of a single Ψ on H69 to its structure and the importance for its interactions with helix 44 and specific tRNAs. Our study suggests that rRNA modification affects translation of mRNAs carrying codon bias due to selective accommodation of tRNAs by the ribosome. Based on the high-resolution structures, we propose a mechanism explaining how the ribosome selects specific tRNAs. | |||||||||
履歴 |
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構造の表示
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 376 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 108.4 KB 108.4 KB | 表示 表示 | ![]() |
画像 | ![]() | 79.6 KB | ||
Filedesc metadata | ![]() | 20.6 KB | ||
その他 | ![]() ![]() ![]() | 336.9 MB 338.8 MB 338.8 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 965.1 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 964.6 KB | 表示 | |
XML形式データ | ![]() | 17.9 KB | 表示 | |
CIF形式データ | ![]() | 21.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 0.85 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
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試料の構成要素
+全体 : 80S RIBOSOME FROM LEISHMANIA MAJOR
+超分子 #1: 80S RIBOSOME FROM LEISHMANIA MAJOR
+分子 #1: LSUa_rRNA_chain_1
+分子 #2: SR1_chain_3
+分子 #3: SR2_chain_4
+分子 #4: SR4_chain_5
+分子 #5: SR6_chain_6
+分子 #6: 5.8S_rRNA_chain_7
+分子 #7: 5S_rRNA_chain_8
+分子 #26: SSU_rRNA_chain_S1
+分子 #27: E-site_tRNA_chain_S4
+分子 #85: LSUb_rRNA_chain_2
+分子 #8: Putative 60S ribosomal protein L2
+分子 #9: Putative ribosomal protein L3
+分子 #10: Putative ribosomal protein L1a
+分子 #11: 60S ribosomal protein L11
+分子 #12: Putative 60S ribosomal protein L9
+分子 #13: Putative 60S ribosomal protein L6
+分子 #14: 60S ribosomal protein L7a
+分子 #15: Putative 60S ribosomal protein L13a
+分子 #16: Putative 60S ribosomal protein L13
+分子 #17: Putative 60S ribosomal protein L23
+分子 #18: Putative 40S ribosomal protein L14
+分子 #19: Putative 60S ribosomal protein L27A/L29
+分子 #20: Ribosomal protein L15
+分子 #21: Putative 60S ribosomal protein L10
+分子 #22: Putative 60S ribosomal protein L5
+分子 #23: 60S ribosomal protein L18
+分子 #24: Putative 60S ribosomal protein L19
+分子 #25: 60S ribosomal protein L18a
+分子 #28: 40S ribosomal protein S3a
+分子 #29: 40S ribosomal protein SA
+分子 #30: Putative 40S ribosomal protein S3
+分子 #31: Putative 40S ribosomal protein S9
+分子 #32: 40S ribosomal protein S4
+分子 #33: 40S ribosomal protein S2
+分子 #34: 40S ribosomal protein S6
+分子 #35: 40S ribosomal protein S5
+分子 #36: 40S ribosomal protein S7
+分子 #37: 40S ribosomal protein S8
+分子 #38: Putative 40S ribosomal protein S16
+分子 #39: Putative ribosomal protein S20
+分子 #40: Putative 40S ribosomal protein S10
+分子 #41: 40S ribosomal protein S14
+分子 #42: Putative 40S ribosomal protein S23
+分子 #43: 40S ribosomal protein S12
+分子 #44: Putative 40S ribosomal protein S18
+分子 #45: Putative ribosomal protein S29
+分子 #46: Putative 40S ribosomal protein S13
+分子 #47: Putative 40S ribosomal protein S11
+分子 #48: Putative 40S ribosomal protein S17
+分子 #49: Putative 40S ribosomal protein S15
+分子 #50: 40S ribosomal protein S19-like protein
+分子 #51: Putative 40S ribosomal protein S21
+分子 #52: 40S ribosomal protein S24
+分子 #53: Putative 60S ribosomal protein L21
+分子 #54: 40S ribosomal protein S25
+分子 #55: Putative 40S ribosomal protein S27-1
+分子 #56: 40S ribosomal protein S26
+分子 #57: Putative 40S ribosomal protein S33
+分子 #58: 40S ribosomal protein S30
+分子 #59: Guanine nucleotide-binding protein subunit beta-like protein
+分子 #60: Putative RNA binding protein
+分子 #61: Putative 40S ribosomal protein S15A
+分子 #62: Putative 60S ribosomal protein L17
+分子 #63: Putative 60S ribosomal protein L22
+分子 #64: Putative 60S ribosomal protein L23a
+分子 #65: Putative 60S ribosomal protein L26
+分子 #66: Putative ribosomal protein L24
+分子 #67: 60S ribosomal protein L27
+分子 #68: Putative 60S ribosomal protein L28
+分子 #69: Putative 60S ribosomal protein L35
+分子 #70: 60S ribosomal protein L29
+分子 #71: Putative 60S ribosomal protein L7
+分子 #72: 60S ribosomal protein L30
+分子 #73: Putative 60S ribosomal subunit protein L31
+分子 #74: 60S ribosomal protein L32
+分子 #75: Putative ribosomal protein l35a
+分子 #76: Putative 60S ribosomal protein L34
+分子 #77: Putative 60S Ribosomal protein L36
+分子 #78: Ribosomal protein L37
+分子 #79: Putative ribosomal protein L38
+分子 #80: Putative 60S ribosomal protein L39
+分子 #81: Ubiquitin-60S ribosomal protein L40
+分子 #82: 60S ribosomal protein L41
+分子 #83: 60S ribosomal protein L37a
+分子 #84: Putative 60S ribosomal protein L44
+分子 #86: MAGNESIUM ION
+分子 #87: POTASSIUM ION
+分子 #88: SODIUM ION
+分子 #89: ZINC ION
+分子 #90: water
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.6 |
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凍結 | 凍結剤: ETHANE |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 0.83 e/Å2 |
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 / 最大 デフォーカス(公称値): 1.3 µm 最小 デフォーカス(公称値): 0.7000000000000001 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
初期モデル | モデルのタイプ: EMDB MAP EMDB ID: |
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最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 2.4 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 212912 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |