+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-14751 | |||||||||
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タイトル | Rabbit 80S ribosome as it decodes the Sec-UGA codon | |||||||||
マップデータ | ||||||||||
試料 |
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キーワード | Selenocysteine / recoding / 80S / RIBOSOME | |||||||||
機能・相同性 | 機能・相同性情報 forebrain neuron development / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits ...forebrain neuron development / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Major pathway of rRNA processing in the nucleolus and cytosol / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal subunit / selenocysteine incorporation / selenocysteine insertion sequence binding / striatum development / negative regulation of RNA splicing / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / laminin receptor activity / exit from mitosis / Ribosomal scanning and start codon recognition / optic nerve development / Translation initiation complex formation / mammalian oogenesis stage / retinal ganglion cell axon guidance / activation-induced cell death of T cells / Protein hydroxylation / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / organelle membrane / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / T cell proliferation involved in immune response / Major pathway of rRNA processing in the nucleolus and cytosol / protein-RNA complex assembly / ribosomal small subunit export from nucleus / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / translation elongation factor activity / Nuclear events stimulated by ALK signaling in cancer / ribonucleoprotein complex binding / cytosolic ribosome / laminin binding / rough endoplasmic reticulum / 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) / gastrulation / MDM2/MDM4 family protein binding / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / mRNA 3'-UTR binding / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / positive regulation of protein-containing complex assembly / placenta development / Regulation of expression of SLITs and ROBOs / modification-dependent protein catabolic process / cytoplasmic ribonucleoprotein granule / spindle / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / positive regulation of canonical Wnt signaling pathway / ribosome biogenesis / ribosome binding / glucose homeostasis / retina development in camera-type eye / virus receptor activity / regulation of translation / 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 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Cricket paralysis virus (ウイルス) / Rattus norvegicus (ドブネズミ) / Oryctolagus cuniculus (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 | Hilal T / Simonovic M / Spahn CMT | |||||||||
資金援助 | ドイツ, 米国, 2件
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引用 | ジャーナル: Science / 年: 2022 タイトル: Structure of the mammalian ribosome as it decodes the selenocysteine UGA codon. 著者: Tarek Hilal / Benjamin Y Killam / Milica Grozdanović / Malgorzata Dobosz-Bartoszek / Justus Loerke / Jörg Bürger / Thorsten Mielke / Paul R Copeland / Miljan Simonović / Christian M T Spahn / 要旨: The elongation of eukaryotic selenoproteins relies on a poorly understood process of interpreting in-frame UGA stop codons as selenocysteine (Sec). We used cryo-electron microscopy to visualize Sec ...The elongation of eukaryotic selenoproteins relies on a poorly understood process of interpreting in-frame UGA stop codons as selenocysteine (Sec). We used cryo-electron microscopy to visualize Sec UGA recoding in mammals. A complex between the noncoding Sec-insertion sequence (SECIS), SECIS-binding protein 2 (SBP2), and 40 ribosomal subunit enables Sec-specific elongation factor eEFSec to deliver Sec. eEFSec and SBP2 do not interact directly but rather deploy their carboxyl-terminal domains to engage with the opposite ends of the SECIS. By using its Lys-rich and carboxyl-terminal segments, the ribosomal protein eS31 simultaneously interacts with Sec-specific transfer RNA (tRNA) and SBP2, which further stabilizes the assembly. eEFSec is indiscriminate toward l-serine and facilitates its misincorporation at Sec UGA codons. Our results support a fundamentally distinct mechanism of Sec UGA recoding in eukaryotes from that in bacteria. | |||||||||
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_14751.map.gz | 105.6 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-14751-v30.xml emd-14751.xml | 130.1 KB 130.1 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_14751_fsc.xml | 17.9 KB | 表示 | FSCデータファイル |
画像 | emd_14751.png | 127.6 KB | ||
Filedesc metadata | emd-14751.cif.gz | 24.7 KB | ||
その他 | emd_14751_additional_1.map.gz emd_14751_half_map_1.map.gz emd_14751_half_map_2.map.gz | 105.6 MB 475.7 MB 475.7 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-14751 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14751 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_14751_validation.pdf.gz | 1.2 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_14751_full_validation.pdf.gz | 1.2 MB | 表示 | |
XML形式データ | emd_14751_validation.xml.gz | 26 KB | 表示 | |
CIF形式データ | emd_14751_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-14751 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-14751 | HTTPS FTP |
-関連構造データ
関連構造データ | 7zjwMC 7zjxC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-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_14751.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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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: 1.017 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
-追加マップ: locally refined map
ファイル | emd_14751_additional_1.map | ||||||||||||
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注釈 | locally refined 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: #1
ファイル | emd_14751_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_14751_half_map_2.map | ||||||||||||
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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-Selenosome
+超分子 #1: 80S-Selenosome
+超分子 #2: eEFSec and SECIS Binding Protein 2
+超分子 #3: Ser-tRNA-Sec
+超分子 #4: CrPV IRES
+超分子 #5: GPX4 SECIS element
+超分子 #6: 80S Ribosome
+分子 #1: eEFSec
+分子 #5: SECIS Binding Protein 2
+分子 #9: 60S ribosomal protein uL2
+分子 #10: 60S ribosomal protein L3
+分子 #11: 60S ribosomal protein L4
+分子 #12: Ribosomal_L18_c domain-containing protein
+分子 #13: 60S ribosomal protein L6
+分子 #14: 60S ribosomal Protein uL30
+分子 #15: 60S ribosomal protein eL8
+分子 #16: 60S ribosomal protein L9
+分子 #17: 60S ribosomal protein L10
+分子 #18: 60S ribosomal protein L11
+分子 #19: 60S ribosomal protein eL13
+分子 #20: 60S ribosomal protein L14
+分子 #21: 60S ribosomal protein L15
+分子 #22: 60S ribosomal protein uL13
+分子 #23: 60S ribosomal protein uL22
+分子 #24: 60S ribosomal Protein eL18
+分子 #25: 60S ribosomal protein L19
+分子 #26: 60S ribosomal protein eL20
+分子 #27: 60S ribosomal protein eL21
+分子 #28: 60S ribosomal protein eL22
+分子 #29: 60S ribosomal protein L23
+分子 #30: 60S ribosomal protein eL24
+分子 #31: 60S ribosomal protein uL23
+分子 #32: 60S ribosomal protein L26
+分子 #33: 60S ribosomal protein L27
+分子 #34: 60S ribosomal protein L27a
+分子 #35: 60S ribosomal protein L29
+分子 #36: 60S ribosomal protein eL30
+分子 #37: 60S ribosomal protein eL31
+分子 #38: 60S ribosomal protein eL32
+分子 #39: 60S ribosomal protein eL33
+分子 #40: 60S ribosomal protein L34
+分子 #41: 60S ribosomal protein uL29
+分子 #42: 60S ribosomal protein L36
+分子 #43: 60S ribosomal protein L37
+分子 #44: 60S ribosomal protein eL38
+分子 #45: 60S ribosomal protein eL39
+分子 #46: 60S ribosomal protein L40
+分子 #47: 60S ribosomal protein eL42
+分子 #48: 60S ribosomal protein eL43
+分子 #49: 60S ribosomal protein eL28
+分子 #50: 60S ribosomal protein P0
+分子 #51: 60S ribosomal protein uL1
+分子 #53: 40S ribosomal protein S27
+分子 #54: 40S ribosomal protein S28
+分子 #55: 40S ribosomal protein S27a
+分子 #56: 40S ribosomal protein S30
+分子 #57: Ribosomal protein eS26
+分子 #58: RACK1
+分子 #59: 40S ribosomal protein uS14
+分子 #60: 40S ribosomal protein SA
+分子 #61: 40S ribosomal protein S3a
+分子 #62: 40S ribosomal protein uS5
+分子 #63: 40S ribosomal protein S3
+分子 #64: 40S ribosomal protein eS4
+分子 #65: Ribosomal protein S5
+分子 #66: 40S ribosomal protein S6
+分子 #67: 40S ribosomal protein S7
+分子 #68: 40S ribosomal protein S8
+分子 #69: 40S ribosomal protein S9
+分子 #70: 40S ribosomal protein eS10
+分子 #71: 40S ribosomal protein S11
+分子 #72: 40S ribosomal protein S12
+分子 #73: 40S ribosomal protein uS15
+分子 #74: 40S ribosomal protein uS11
+分子 #75: 40S ribosomal protein uS19
+分子 #76: 40S ribosomal protein uS9
+分子 #77: 40S ribosomal protein eS17
+分子 #78: 40S ribosomal protein S18
+分子 #79: 40S Ribosomal protein eS19
+分子 #80: 40S ribosomal protein uS10
+分子 #81: 40S ribosomal protein eS21
+分子 #82: 40S ribosomal protein S15a
+分子 #83: 40S ribosomal protein S23
+分子 #84: 40S ribosomal protein S24
+分子 #85: 40S ribosomal protein S25
+分子 #86: 60S ribosomal protein L41
+分子 #2: human Ser-tRNA-Sec
+分子 #3: CrPV IRES
+分子 #4: GPX4 SECIS element
+分子 #6: 28S rRNA
+分子 #7: 5S rRNA
+分子 #8: 5.8S rRNA
+分子 #52: 18S rRNA
+分子 #87: GUANOSINE-5'-TRIPHOSPHATE
+分子 #88: SERINE
+分子 #89: MAGNESIUM ION
+分子 #90: POTASSIUM ION
+分子 #91: ZINC ION
+分子 #92: SODIUM ION
+分子 #93: 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 R3/3 / 材質: COPPER/RHODIUM / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 45 sec. |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / 装置: FEI VITROBOT MARK II |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 撮影したグリッド数: 1 / 実像数: 13921 / 平均電子線量: 30.0 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 / 最大 デフォーカス(公称値): 2.0 µm / 最小 デフォーカス(公称値): 0.8 µm |
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 |