+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-23785 | |||||||||
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タイトル | 80S rabbit ribosome stalled with benzamide-CHX | |||||||||
マップデータ | sharpened map | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 regulation of G1 to G0 transition / laminin receptor activity / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage ...regulation of G1 to G0 transition / laminin receptor activity / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / phagocytic cup / ubiquitin ligase inhibitor activity / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / T cell proliferation involved in immune response / protein-RNA complex assembly / erythrocyte development / negative regulation of ubiquitin-dependent protein catabolic process / translation regulator activity / cellular response to actinomycin D / ribosomal small subunit export from nucleus / cytosolic ribosome / laminin binding / 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) / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / positive regulation of apoptotic signaling pathway / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / small-subunit processome / positive regulation of translation / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / transcription coactivator binding / mRNA 5'-UTR binding / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / rRNA processing / G1/S transition of mitotic cell cycle / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of canonical Wnt signaling pathway / rhythmic process / ribosome binding / retina development in camera-type eye / glucose homeostasis / regulation of translation / virus receptor activity / heparin binding / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / perikaryon / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / killing of cells of another organism / cytoplasmic translation / mitochondrial inner membrane / tRNA binding / postsynaptic density / cell differentiation / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell division / DNA repair / mRNA binding / centrosome / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Rabbit (ウサギ) / synthetic construct (人工物) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.2 Å | |||||||||
データ登録者 | Koga Y / Hoang EM / Park Y / Keszei AFA / Murray J / Shao S / Liau BB | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: J Am Chem Soc / 年: 2021 タイトル: Discovery of C13-Aminobenzoyl Cycloheximide Derivatives that Potently Inhibit Translation Elongation. 著者: Yumi Koga / Eileen M Hoang / Yongho Park / Alexander F A Keszei / Jason Murray / Sichen Shao / Brian B Liau / 要旨: Employed for over half a century to study protein synthesis, cycloheximide (CHX, ) is a small molecule natural product that reversibly inhibits translation elongation. More recently, CHX has been ...Employed for over half a century to study protein synthesis, cycloheximide (CHX, ) is a small molecule natural product that reversibly inhibits translation elongation. More recently, CHX has been applied to ribosome profiling, a method for mapping ribosome positions on mRNA genome-wide. Despite CHX's extensive use, CHX treatment often results in incomplete translation inhibition due to its rapid reversibility, prompting the need for improved reagents. Here, we report the concise synthesis of C13-amide-functionalized CHX derivatives with increased potencies toward protein synthesis inhibition. Cryogenic electron microscopy (cryo-EM) revealed that C13-aminobenzoyl CHX () occupies the same site as CHX, competing with the 3' end of E-site tRNA. We demonstrate that is superior to CHX for ribosome profiling experiments, enabling more effective capture of ribosome conformations through sustained stabilization of polysomes. Our studies identify powerful chemical reagents to study protein synthesis and reveal the molecular basis of their enhanced potency. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_23785.map.gz | 19.2 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-23785-v30.xml emd-23785.xml | 94.5 KB 94.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_23785_fsc.xml | 12.8 KB | 表示 | FSCデータファイル |
画像 | emd_23785.png | 204 KB | ||
その他 | emd_23785_additional_1.map.gz emd_23785_half_map_1.map.gz emd_23785_half_map_2.map.gz | 154.7 MB 159.6 MB 159.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-23785 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23785 | 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_23785.map.gz / 形式: CCP4 / 大きさ: 178 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | sharpened map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-追加マップ: unsharpened map
ファイル | emd_23785_additional_1.map | ||||||||||||
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注釈 | unsharpened 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: half1 map
ファイル | emd_23785_half_map_1.map | ||||||||||||
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注釈 | half1 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: half2 map
ファイル | emd_23785_half_map_2.map | ||||||||||||
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注釈 | half2 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 : 80S rabbit ribosome stalled with benzamide-CHX
+超分子 #1: 80S rabbit ribosome stalled with benzamide-CHX
+分子 #1: Ribosomal protein L8
+分子 #2: uL3
+分子 #3: 60S ribosomal protein L4
+分子 #4: Ribosomal_L18_c domain-containing protein
+分子 #5: 60S ribosomal protein L6
+分子 #6: 60S ribosomal protein L7
+分子 #7: 60S ribosomal protein L7a
+分子 #8: 60S ribosomal protein L9
+分子 #9: 60S ribosomal protein L10
+分子 #10: 60S ribosomal protein L11
+分子 #11: 60S ribosomal protein L13
+分子 #12: 60S ribosomal protein L14
+分子 #13: Ribosomal protein L15
+分子 #14: uL13
+分子 #15: uL22
+分子 #16: Ribosomal protein L18
+分子 #17: Ribosomal protein L19
+分子 #18: 60S ribosomal protein L18a
+分子 #19: eL21
+分子 #20: eL22
+分子 #21: Ribosomal protein L23
+分子 #22: 60S ribosomal protein L24
+分子 #23: eL23
+分子 #24: uL24
+分子 #25: 60S ribosomal protein L27
+分子 #26: 60S ribosomal protein L27a
+分子 #27: 60S ribosomal protein L29
+分子 #28: eL30
+分子 #29: eL31
+分子 #30: eL32
+分子 #31: eL33
+分子 #32: 60S ribosomal protein L34
+分子 #33: eL35
+分子 #34: 60S ribosomal protein L36
+分子 #35: Ribosomal protein L37
+分子 #36: 60S ribosomal protein L38
+分子 #37: eL39
+分子 #38: eL40
+分子 #39: 60s ribosomal protein l41
+分子 #40: eL42
+分子 #41: eL43
+分子 #42: eL28
+分子 #43: 40S ribosomal protein SA
+分子 #44: eS1
+分子 #45: uS5
+分子 #46: Ribosomal protein S3
+分子 #47: 40S ribosomal protein S4
+分子 #48: uS7
+分子 #49: eS6
+分子 #50: eS7
+分子 #51: eS8
+分子 #52: uS4
+分子 #53: S10_plectin domain-containing protein
+分子 #54: uS17
+分子 #55: eS12
+分子 #56: uS15
+分子 #57: uS11
+分子 #58: uS19
+分子 #59: uS9
+分子 #60: eS17
+分子 #61: uS13
+分子 #62: eS19
+分子 #63: uS10
+分子 #64: 40S ribosomal protein S21
+分子 #65: uS8
+分子 #66: uS12
+分子 #67: 40S ribosomal protein S24
+分子 #68: eS25
+分子 #69: 40S ribosomal protein S26
+分子 #70: eS27
+分子 #71: eS28
+分子 #72: eS29
+分子 #73: eS30
+分子 #74: eS31
+分子 #75: RACK1
+分子 #76: 28S rRNA
+分子 #77: 5S rRNA
+分子 #78: 5.8S rRNA
+分子 #79: P-site tRNA
+分子 #80: 18S rRNA
+分子 #81: mRNA
+分子 #82: MAGNESIUM ION
+分子 #83: ZINC ION
+分子 #84: N-[(1R,3S,4R,5S)-3-{(1R)-2-[(2R,4r,6S)-2,6-dihydroxypiperidin-4-y...
-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
濃度 | 0.5 mg/mL |
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緩衝液 | pH: 7.4 |
グリッド | モデル: Quantifoil / 材質: COPPER / メッシュ: 400 / 前処理 - タイプ: GLOW DISCHARGE |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK II / 詳細: 3 sec blot. |
-電子顕微鏡法
顕微鏡 | FEI POLARA 300 |
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撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 検出モード: SUPER-RESOLUTION / 平均電子線量: 47.0 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 |
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |