+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-10181 | ||||||||||||||||||
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タイトル | Rabbit 80S ribosome stalled on a poly(A) tail | ||||||||||||||||||
マップデータ | Structure of rabbit 80S stalled on a polyA tail | ||||||||||||||||||
試料 |
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機能・相同性 | 機能・相同性情報 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 / retinal ganglion cell axon guidance / mammalian oogenesis stage / 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 / 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 / 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 / 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 / placenta development / small-subunit processome / positive regulation of translation / protein kinase C binding / positive regulation of protein-containing complex assembly / G1/S transition of mitotic cell cycle / cellular response to gamma radiation / transcription coactivator binding / mRNA 5'-UTR binding / modification-dependent protein catabolic process / spindle / cytoplasmic ribonucleoprotein granule / positive regulation of canonical Wnt signaling pathway / rhythmic process / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / ribosome binding / 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 / cytosolic small ribosomal subunit / perikaryon / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / killing of cells of another organism / cytoplasmic translation / cell differentiation / tRNA binding / postsynaptic density / protein stabilization / rRNA binding / mitochondrial inner membrane / ribosome / protein ubiquitination / structural constituent of ribosome / translation / positive regulation of protein phosphorylation / ribonucleoprotein complex / positive regulation of apoptotic process / cell division / DNA repair / centrosome / mRNA binding / positive regulation of cell population proliferation / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of gene expression / negative regulation of apoptotic process / nucleolus / protein kinase binding / apoptotic process / perinuclear region of cytoplasm 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / Homo sapiens (ヒト) / Rabbit (ウサギ) | ||||||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.8 Å | ||||||||||||||||||
データ登録者 | Chandrasekaran V / Juszkiewicz S / Choi J / Puglisi JD / Brown A / Shao S / Ramakrishnan V / Hegde RS | ||||||||||||||||||
資金援助 | 英国, 米国, 5件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2019 タイトル: Mechanism of ribosome stalling during translation of a poly(A) tail. 著者: Viswanathan Chandrasekaran / Szymon Juszkiewicz / Junhong Choi / Joseph D Puglisi / Alan Brown / Sichen Shao / V Ramakrishnan / Ramanujan S Hegde / 要旨: Faulty or damaged messenger RNAs are detected by the cell when translating ribosomes stall during elongation and trigger pathways of mRNA decay, nascent protein degradation and ribosome recycling. ...Faulty or damaged messenger RNAs are detected by the cell when translating ribosomes stall during elongation and trigger pathways of mRNA decay, nascent protein degradation and ribosome recycling. The most common mRNA defect in eukaryotes is probably inappropriate polyadenylation at near-cognate sites within the coding region. How ribosomes stall selectively when they encounter poly(A) is unclear. Here, we use biochemical and structural approaches in mammalian systems to show that poly-lysine, encoded by poly(A), favors a peptidyl-transfer RNA conformation suboptimal for peptide bond formation. This conformation partially slows elongation, permitting poly(A) mRNA in the ribosome's decoding center to adopt a ribosomal RNA-stabilized single-stranded helix. The reconfigured decoding center clashes with incoming aminoacyl-tRNA, thereby precluding elongation. Thus, coincidence detection of poly-lysine in the exit tunnel and poly(A) in the decoding center allows ribosomes to detect aberrant mRNAs selectively, stall elongation and trigger downstream quality control pathways essential for cellular homeostasis. | ||||||||||||||||||
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_10181.map.gz | 63.5 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-10181-v30.xml emd-10181.xml | 112.4 KB 112.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_10181_fsc.xml | 18 KB | 表示 | FSCデータファイル |
画像 | emd_10181.png | 271.8 KB | ||
マスクデータ | emd_10181_msk_1.map | 512 MB | マスクマップ | |
その他 | emd_10181_additional.map.gz emd_10181_half_map_1.map.gz emd_10181_half_map_2.map.gz | 411.2 MB 413.5 MB 413.5 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-10181 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10181 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_10181_validation.pdf.gz | 486.8 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_10181_full_validation.pdf.gz | 486.4 KB | 表示 | |
XML形式データ | emd_10181_validation.xml.gz | 26.2 KB | 表示 | |
CIF形式データ | emd_10181_validation.cif.gz | 34.6 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10181 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10181 | 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_10181.map.gz / 形式: CCP4 / 大きさ: 512 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | Structure of rabbit 80S stalled on a polyA tail | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.085 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
-マスク #1
ファイル | emd_10181_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Unsharpened map
ファイル | emd_10181_additional.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_10181_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_10181_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 : Rabbit 80S ribosome stalled on polyA mRNA
+超分子 #1: Rabbit 80S ribosome stalled on polyA mRNA
+超分子 #2: ribosome
+超分子 #3: polyA mRNA
+分子 #1: 18S ribosomal RNA
+分子 #35: polyA mRNA
+分子 #80: 28S ribosomal RNA
+分子 #81: 5S ribosomal RNA
+分子 #82: 5.8S ribosomal RNA
+分子 #85: tRNA (Lys3)
+分子 #2: uS2
+分子 #3: 40S ribosomal protein S3a
+分子 #4: uS5
+分子 #5: uS5
+分子 #6: 40S ribosomal protein S4
+分子 #7: Ribosomal protein S5
+分子 #8: 40S ribosomal protein S6
+分子 #9: 40S ribosomal protein S7
+分子 #10: 40S ribosomal protein S8
+分子 #11: Ribosomal protein S9 (Predicted)
+分子 #12: S10_plectin domain-ontaining protein
+分子 #13: Ribosomal protein S11
+分子 #14: 40S ribosomal protein S12
+分子 #15: Ribosomal_S13_N domain-containing protein
+分子 #16: uS11
+分子 #17: uS19
+分子 #18: Ribosomal protein S16
+分子 #19: eS17
+分子 #20: eS13
+分子 #21: eS19
+分子 #22: Ribosomal_S10 domain-containing protein
+分子 #23: eS21
+分子 #24: Ribosomal protein S15a
+分子 #25: uS12
+分子 #26: eS24
+分子 #27: eS25
+分子 #28: eS26
+分子 #29: 40S ribosomal protein S27
+分子 #30: Ribosomal protein S28
+分子 #31: uS14
+分子 #32: 40S ribosomal protein S30
+分子 #33: Ribosomal protein S27a
+分子 #34: WD_REPEATS_REGION domain-containing protein
+分子 #36: Ribosomal protein L8
+分子 #37: uL3
+分子 #38: uL4
+分子 #39: 60S ribosomal protein L5
+分子 #40: 60S ribosomal protein L6
+分子 #41: uL30
+分子 #42: eL8
+分子 #43: uL6
+分子 #44: 60S ribosomal protein L10
+分子 #45: Ribosomal protein L11
+分子 #46: eL13
+分子 #47: Ribosomal protein L14
+分子 #48: Ribosomal protein L15
+分子 #49: uL13
+分子 #50: uL22
+分子 #51: eL18
+分子 #52: eL19
+分子 #53: eL20
+分子 #54: eL21
+分子 #55: eL22
+分子 #56: Ribosomal protein L23
+分子 #57: TRASH domain-containing protein
+分子 #58: Ribosomal_L23eN domain-containing protein
+分子 #59: Ribosomal protein L26
+分子 #60: 60S ribosomal protein L27
+分子 #61: Ribosomal_L18e/L15P domain-containing protein
+分子 #62: eL29
+分子 #63: Ribosomal_L7Ae domain-containing protein
+分子 #64: eL31
+分子 #65: eL32
+分子 #66: eL33
+分子 #67: eL34
+分子 #68: uL29
+分子 #69: 60S ribosomal protein L36
+分子 #70: Ribosomal protein L37
+分子 #71: eL38
+分子 #72: eL39
+分子 #73: eL40
+分子 #74: 60s ribosomal protein l41
+分子 #75: eL42
+分子 #76: eL43
+分子 #77: Ribosomal_L28e domain-containing protein
+分子 #78: uL10
+分子 #79: Ribosomal protein L12
+分子 #83: poly-lysine nascent chain
+分子 #84: Ribosomal protein
+分子 #86: MAGNESIUM ION
+分子 #87: ZINC ION
+分子 #88: SPERMIDINE
-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: 7.4 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | #0 - Image recording ID: 1 #0 - フィルム・検出器のモデル: FEI FALCON III (4k x 4k) #0 - 検出モード: INTEGRATING / #0 - 平均電子線量: 41.8 e/Å2 / #1 - Image recording ID: 2 #1 - フィルム・検出器のモデル: FEI FALCON III (4k x 4k) #1 - 平均電子線量: 41.8 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: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: FLEXIBLE FIT |
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得られたモデル | PDB-6sgc: |