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データを開く
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基本情報
登録情報 | データベース: EMDB / ID: EMD-9239 | |||||||||
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タイトル | Rabbit 80S ribosome with Z-site tRNA and IFRD2 (unrotated state) | |||||||||
![]() | Postprocessed map | |||||||||
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機能・相同性 | ![]() regulation of G1 to G0 transition / 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 / mammalian oogenesis stage / retinal ganglion cell axon guidance / G1 to G0 transition ...regulation of G1 to G0 transition / 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 / mammalian oogenesis stage / retinal ganglion cell axon guidance / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / TOR signaling / T cell proliferation involved in immune response / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cellular response to actinomycin D / cytosolic ribosome / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / negative regulation of ubiquitin-dependent protein catabolic process / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of LSU-rRNA / ribosomal large subunit biogenesis / maturation of SSU-rRNA / positive regulation of translation / small-subunit processome / protein kinase C binding / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / protein tag activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosome binding / glucose homeostasis / retina development in camera-type eye / regulation of translation / 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 / perikaryon / cytosolic small ribosomal subunit / defense response to Gram-negative bacterium / killing of cells of another organism / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / 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 cycle / centrosome / mRNA binding / apoptotic process / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression / nucleolus / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding / cytoplasm / cytosol 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: 3.4 Å | |||||||||
![]() | Brown A / Baird MR / Yip MCJ / Murray J / Shao S | |||||||||
![]() | ![]() タイトル: Structures of translationally inactive mammalian ribosomes. 著者: Alan Brown / Matthew R Baird / Matthew Cj Yip / Jason Murray / Sichen Shao / ![]() ![]() 要旨: The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. ...The cellular levels and activities of ribosomes directly regulate gene expression during numerous physiological processes. The mechanisms that globally repress translation are incompletely understood. Here, we use electron cryomicroscopy to analyze inactive ribosomes isolated from mammalian reticulocytes, the penultimate stage of red blood cell differentiation. We identify two types of ribosomes that are translationally repressed by protein interactions. The first comprises ribosomes sequestered with elongation factor 2 (eEF2) by SERPINE mRNA binding protein 1 (SERBP1) occupying the ribosomal mRNA entrance channel. The second type are translationally repressed by a novel ribosome-binding protein, interferon-related developmental regulator 2 (IFRD2), which spans the P and E sites and inserts a C-terminal helix into the mRNA exit channel to preclude translation. IFRD2 binds ribosomes with a tRNA occupying a noncanonical binding site, the 'Z site', on the ribosome. These structures provide functional insights into how ribosomal interactions may suppress translation to regulate gene expression. | |||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | EMマップ: ![]() ![]() ![]() |
添付画像 |
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ダウンロードとリンク
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マップデータ | ![]() | 16.4 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 96.6 KB 96.6 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 14.1 KB | 表示 | ![]() |
画像 | ![]() | 174.1 KB | ||
その他 | ![]() ![]() ![]() | 214.8 MB 215.2 MB 214.9 MB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 660.3 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 659.9 KB | 表示 | |
XML形式データ | ![]() | 22.2 KB | 表示 | |
CIF形式データ | ![]() | 29.1 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 6mtcMC ![]() 9234C ![]() 9235C ![]() 9236C ![]() 9237C ![]() 9240C ![]() 9241C ![]() 9242C ![]() 6mtbC ![]() 6mtdC ![]() 6mteC C: 同じ文献を引用 ( M: このマップから作成された原子モデル |
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リンク
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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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注釈 | Postprocessed map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: Pre-postprocessed map
ファイル | emd_9239_additional.map | ||||||||||||
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注釈 | Pre-postprocessed 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
ファイル | emd_9239_half_map_1.map | ||||||||||||
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注釈 | Half map 1 | ||||||||||||
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 2
ファイル | emd_9239_half_map_2.map | ||||||||||||
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注釈 | Half map 2 | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : Rabbit 80S ribosome with Z-site tRNA and IFRD2
+超分子 #1: Rabbit 80S ribosome with Z-site tRNA and IFRD2
+分子 #1: Z-site tRNA
+分子 #2: 28S rRNA
+分子 #3: 5S rRNA
+分子 #4: 5.8S rRNA
+分子 #49: 18S rRNA
+分子 #5: 60S ribosomal protein L8
+分子 #6: 60S ribosomal protein L3
+分子 #7: 60S ribosomal protein L4
+分子 #8: 60S ribosomal protein L5
+分子 #9: 60S ribosomal protein L6
+分子 #10: 60S ribosomal protein L7
+分子 #11: 60S ribosomal protein L7a
+分子 #12: 60S ribosomal protein L9
+分子 #13: 60S ribosomal protein L10
+分子 #14: 60S ribosomal protein L11
+分子 #15: 60S ribosomal protein L13
+分子 #16: 60S ribosomal protein L14
+分子 #17: 60S Ribosomal protein L15
+分子 #18: 60S ribosomal protein L13a
+分子 #19: 60S ribosomal protein L17
+分子 #20: 60S ribosomal protein L18
+分子 #21: 60S ribosomal protein L19
+分子 #22: 60S ribosomal protein L18a
+分子 #23: 60S ribosomal protein L21
+分子 #24: 60S ribosomal protein L22
+分子 #25: 60S ribosomal protein L23
+分子 #26: 60S ribosomal protein L24
+分子 #27: 60S ribosomal protein L23a
+分子 #28: 60S ribosomal protein L26
+分子 #29: 60S ribosomal protein L27
+分子 #30: 60S ribosomal protein L27a
+分子 #31: 60S ribosomal protein L29
+分子 #32: 60S ribosomal protein L30
+分子 #33: 60S ribosomal protein L31
+分子 #34: 60S ribosomal protein L32
+分子 #35: 60S ribosomal protein L35a
+分子 #36: 60S ribosomal protein L34
+分子 #37: 60S ribosomal protein L35
+分子 #38: 60S ribosomal protein L36
+分子 #39: 60S ribosomal protein L37
+分子 #40: 60S ribosomal protein L38
+分子 #41: 60S ribosomal protein L39
+分子 #42: 60S ribosomal protein L40
+分子 #43: 60S ribosomal protein L41
+分子 #44: 60S ribosomal protein L36a
+分子 #45: 60S ribosomal protein L37a
+分子 #46: 60S ribosomal protein L28
+分子 #47: 60S ribosomal protein L10a
+分子 #48: Interferon-related developmental regulator 2
+分子 #50: 40S ribosomal protein SA
+分子 #51: 40S ribosomal protein S3a
+分子 #52: 40S ribosomal protein S2
+分子 #53: 40S ribosomal protein S3
+分子 #54: 40S ribosomal protein S4, X isoform
+分子 #55: 40S ribosomal protein S5
+分子 #56: 40S ribosomal protein S6
+分子 #57: 40S ribosomal protein S7
+分子 #58: 40S ribosomal protein S8
+分子 #59: 40S ribosomal protein S9
+分子 #60: 40S ribosomal protein S10
+分子 #61: 40S ribosomal protein S11
+分子 #62: 40S ribosomal protein S12
+分子 #63: 40S ribosomal protein S13
+分子 #64: 40S ribosomal protein S14
+分子 #65: 40S ribosomal protein S15
+分子 #66: 40S ribosomal protein S16
+分子 #67: 40S ribosomal protein S17
+分子 #68: 40S ribosomal protein S18
+分子 #69: 40S ribosomal protein S19
+分子 #70: 40S ribosomal protein S20
+分子 #71: 40S ribosomal protein S21
+分子 #72: 40S ribosomal protein S15a
+分子 #73: 40S ribosomal protein S23
+分子 #74: 40S ribosomal protein S24
+分子 #75: 40S ribosomal protein S25
+分子 #76: 40S ribosomal protein S26
+分子 #77: 40S ribosomal protein S27
+分子 #78: 40S ribosomal protein S28
+分子 #79: 40S ribosomal protein S29
+分子 #80: 40S ribosomal protein S30
+分子 #81: 40S ribosomal protein S27a
+分子 #82: Receptor of activated protein C kinase 1
+分子 #83: MAGNESIUM ION
+分子 #84: ZINC ION
-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: 7.4 |
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グリッド | モデル: Quantifoil R2/2 / 材質: COPPER / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: CONTINUOUS / 支持フィルム - Film thickness: 5.0 nm |
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 |
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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: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / デジタル化 - 画像ごとのフレーム数: 1-17 / 平均露光時間: 1.1 sec. / 平均電子線量: 40.0 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 / Cs: 2.7 mm |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |