+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-19576 | |||||||||
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タイトル | CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA : PARENTAL STRAIN | |||||||||
マップデータ | Post_processed consensus map | |||||||||
試料 |
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キーワード | CRYO-EM / LEISHMANIA MAJOR / 80S / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 ciliary transition zone / nuclear lumen / ciliary plasm / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / 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) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome ...ciliary transition zone / nuclear lumen / ciliary plasm / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / translation regulator activity / 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) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / 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 / protein kinase C binding / maintenance of translational fidelity / modification-dependent protein catabolic process / protein tag activity / rRNA processing / ribosomal small subunit biogenesis / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / kinase activity / ribosomal small subunit assembly / small ribosomal subunit / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / negative regulation of translation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of protein phosphorylation / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | Leishmania major strain Friedlin (大形リーシュマニア) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.93 Å | |||||||||
データ登録者 | Rajan KS / Yonath A | |||||||||
資金援助 | European Union, 1件
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引用 | ジャーナル: Cell Rep / 年: 2024 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
添付画像 |
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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 | emd_19576.map.gz | 390.9 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-19576-v30.xml emd-19576.xml | 109.9 KB 109.9 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_19576_fsc.xml | 17 KB | 表示 | FSCデータファイル |
画像 | emd_19576.png | 62.6 KB | ||
Filedesc metadata | emd-19576.cif.gz | 21 KB | ||
その他 | emd_19576_half_map_1.map.gz emd_19576_half_map_2.map.gz | 333.3 MB 333.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-19576 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19576 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_19576_validation.pdf.gz | 1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_19576_full_validation.pdf.gz | 1 MB | 表示 | |
XML形式データ | emd_19576_validation.xml.gz | 25.8 KB | 表示 | |
CIF形式データ | emd_19576_validation.cif.gz | 32.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19576 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19576 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_19576.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Post_processed consensus map | ||||||||||||||||||||||||||||||||||||
投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.8245 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
-ハーフマップ: Half map 2 of consensus map
ファイル | emd_19576_half_map_1.map | ||||||||||||
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注釈 | Half map 2 of consensus map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Half map 1 of consensus map
ファイル | emd_19576_half_map_2.map | ||||||||||||
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注釈 | Half map 1 of consensus map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-sit...
+超分子 #1: CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-sit...
+分子 #1: LSUa_rRNA_chain_1
+分子 #2: LSUb_rRNA_chain_2
+分子 #3: SR1_chain_3
+分子 #4: SR2_chain_4
+分子 #5: SR4_chain_5
+分子 #6: SR6_chain_6
+分子 #7: 5.8S_rRNA_chain_7
+分子 #8: 5S_rRNA_chain_8
+分子 #51: SSU_rRNA_chain_S1
+分子 #52: A-site_tRNA_chain_S2
+分子 #53: P-site_tRNA_chain_S3
+分子 #54: E-site_tRNA_chain_S4
+分子 #55: mRNA_chain_S5
+分子 #9: Putative 60S ribosomal protein L2
+分子 #10: Putative ribosomal protein L3
+分子 #11: Putative ribosomal protein L1a
+分子 #12: 60S ribosomal protein L11
+分子 #13: Putative 60S ribosomal protein L9
+分子 #14: Putative 60S ribosomal protein L6
+分子 #15: 60S ribosomal protein L7a
+分子 #16: Putative 60S ribosomal protein L13a
+分子 #17: Putative 60S ribosomal protein L13
+分子 #18: Putative 60S ribosomal protein L23
+分子 #19: Putative 40S ribosomal protein L14
+分子 #20: Putative 60S ribosomal protein L27A/L29
+分子 #21: Ribosomal protein L15
+分子 #22: Putative 60S ribosomal protein L10
+分子 #23: Putative 60S ribosomal protein L5
+分子 #24: 60S ribosomal protein L18
+分子 #25: Putative 60S ribosomal protein L19
+分子 #26: 60S ribosomal protein L18a
+分子 #27: Putative 60S ribosomal protein L21
+分子 #28: Putative 60S ribosomal protein L17
+分子 #29: Putative 60S ribosomal protein L22
+分子 #30: Putative 60S ribosomal protein L23a
+分子 #31: Putative 60S ribosomal protein L26
+分子 #32: Putative ribosomal protein L24
+分子 #33: 60S ribosomal protein L27
+分子 #34: Putative 60S ribosomal protein L28
+分子 #35: Putative 60S ribosomal protein L35
+分子 #36: 60S ribosomal protein L29
+分子 #37: Putative 60S ribosomal protein L7
+分子 #38: 60S ribosomal protein L30
+分子 #39: Putative 60S ribosomal subunit protein L31
+分子 #40: 60S ribosomal protein L32
+分子 #41: Putative ribosomal protein l35a
+分子 #42: Putative 60S ribosomal protein L34
+分子 #43: Putative 60S Ribosomal protein L36
+分子 #44: Ribosomal protein L37
+分子 #45: Putative ribosomal protein L38
+分子 #46: Putative 60S ribosomal protein L39
+分子 #47: Ubiquitin-60S ribosomal protein L40
+分子 #48: 60S ribosomal protein L41
+分子 #49: 60S ribosomal protein L37a
+分子 #50: Putative 60S ribosomal protein L44
+分子 #56: 40S ribosomal protein S3a
+分子 #57: 40S ribosomal protein SA
+分子 #58: Putative 40S ribosomal protein S3
+分子 #59: Putative 40S ribosomal protein S9
+分子 #60: 40S ribosomal protein S4
+分子 #61: 40S ribosomal protein S2
+分子 #62: 40S ribosomal protein S6
+分子 #63: 40S ribosomal protein S5
+分子 #64: 40S ribosomal protein S7
+分子 #65: Putative 40S ribosomal protein S15A
+分子 #66: 40S ribosomal protein S8
+分子 #67: Putative 40S ribosomal protein S16
+分子 #68: Putative ribosomal protein S20
+分子 #69: Putative 40S ribosomal protein S10
+分子 #70: 40S ribosomal protein S14
+分子 #71: Putative 40S ribosomal protein S23
+分子 #72: 40S ribosomal protein S12
+分子 #73: Putative 40S ribosomal protein S18
+分子 #74: Putative ribosomal protein S29
+分子 #75: Putative 40S ribosomal protein S13
+分子 #76: Ribosomal protein S17 family protein
+分子 #77: Putative 40S ribosomal protein S17
+分子 #78: Putative 40S ribosomal protein S15
+分子 #79: 40S ribosomal protein S19-like protein
+分子 #80: Putative 40S ribosomal protein S21
+分子 #81: 40S ribosomal protein S24
+分子 #82: 40S ribosomal protein S25
+分子 #83: 40S ribosomal protein S26
+分子 #84: Putative 40S ribosomal protein S27-1
+分子 #85: Putative 40S ribosomal protein S33
+分子 #86: 40S ribosomal protein S30
+分子 #87: Ubiquitin-60S ribosomal protein L40
+分子 #88: Guanine nucleotide-binding protein subunit beta-like protein
+分子 #89: Putative RNA binding protein
+分子 #90: MAGNESIUM ION
+分子 #91: SODIUM ION
+分子 #92: POTASSIUM ION
+分子 #93: (2S)-2-[2-[4-[[(2R,3S,4S)-3-acetyloxy-4-oxidanyl-pyrrolidin-2-yl]...
+分子 #94: ZINC ION
+分子 #95: 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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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.6 |
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グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY |
凍結 | 凍結剤: ETHANE |
詳細 | CRYO-EM STRUCTURE OF LEISHMANIA MAJOR 80S RIBOSOME WITH A/P/E-site tRNA AND mRNA |
-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: 0.9340390798620625 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
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): 1.7 µm / 最小 デフォーカス(公称値): 0.6 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |