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データを開く
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基本情報
| 登録情報 | ![]() | |||||||||||||||
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| タイトル | Rabbit 80S ribosome in complex with eRF1-AAQ, stalled at the Stop codon in mutated F2A sequence | |||||||||||||||
マップデータ | Sharpened, masked map (using B-factor of -10 and provided mask) | |||||||||||||||
試料 |
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キーワード | Translation / Recoding / Nascent peptide / Foot-and-mouth disease virus / F2A / StopGo / RIBOSOME | |||||||||||||||
| 機能・相同性 | 機能・相同性情報[histone H4]-N-methyl-L-lysine20 N-methyltransferase / regulation of macromolecule metabolic process / L-peptidase / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H4K20me methyltransferase activity / translation termination factor activity / translation release factor complex / cytoplasmic translational termination / symbiont-mediated perturbation of host chromatin organization ...[histone H4]-N-methyl-L-lysine20 N-methyltransferase / regulation of macromolecule metabolic process / L-peptidase / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H4K20me methyltransferase activity / translation termination factor activity / translation release factor complex / cytoplasmic translational termination / symbiont-mediated perturbation of host chromatin organization / regulation of translational termination / translation release factor activity / translation release factor activity, codon specific / protein methylation / S-adenosyl-L-methionine binding / sequence-specific mRNA binding / peptidyl-tRNA hydrolase activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of double-strand break repair via nonhomologous end joining / laminin receptor activity / Protein hydroxylation / Eukaryotic Translation Termination / 90S preribosome / ubiquitin ligase inhibitor activity / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / pericentric heterochromatin / translational termination / phagocytic cup / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein-RNA complex assembly / translation regulator activity / rough endoplasmic reticulum / ribosomal small subunit export from nucleus / laminin binding / gastrulation / MDM2/MDM4 family protein binding / cytosolic ribosome / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / ribosomal large subunit biogenesis / 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) / maturation of SSU-rRNA / picornain 3C / small-subunit processome / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / spindle / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / rRNA processing / ribonucleoside triphosphate phosphatase activity / positive regulation of canonical Wnt signaling pathway / rhythmic process / regulation of translation / antimicrobial humoral immune response mediated by antimicrobial peptide / heparin binding / nucleoside-triphosphate phosphatase / large ribosomal subunit / ribosomal small subunit assembly / virus receptor activity / ribosome binding / channel activity / ribosomal small subunit biogenesis / 5S rRNA binding / small ribosomal subunit / ribosomal large subunit assembly / small ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / methylation / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / killing of cells of another organism / cytosolic large ribosomal subunit / defense response to Gram-negative bacterium / perikaryon / cytoplasmic translation / cell differentiation / tRNA binding / RNA helicase activity / mitochondrial inner membrane / negative regulation of translation / postsynaptic density / rRNA binding / viral protein processing / structural constituent of ribosome / host cell endoplasmic reticulum membrane / ribosome / translation / ribonucleoprotein complex / cell division / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / DNA repair / RNA-directed RNA polymerase activity / mRNA binding 類似検索 - 分子機能 | |||||||||||||||
| 生物種 | ![]() Foot-and-mouth disease virus SAT 2 (ウイルス) / Homo sapiens (ヒト) | |||||||||||||||
| 手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.65 Å | |||||||||||||||
データ登録者 | Li X / Zuber PK / Loughran G / Bhatt PR / Alquraish F / Ramakrishnan V / Firth AE / Atkins JF | |||||||||||||||
| 資金援助 | 英国, European Union, 4件
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引用 | ジャーナル: Proc Natl Acad Sci U S A / 年: 2026タイトル: Molecular architecture and diversity of StopGo/2A translational recoding. 著者: Xueyan Li / Philipp K Zuber / Gary Loughran / Pramod R Bhatt / Fatema Alquraish / V Ramakrishnan / Andrew E Firth / John F Atkins / ![]() 要旨: Viral 2A sequences trigger a cotranslational peptide bond formation "skipping" event, termed "StopGo," to generate two separate proteins from a single open reading frame without classical termination. ...Viral 2A sequences trigger a cotranslational peptide bond formation "skipping" event, termed "StopGo," to generate two separate proteins from a single open reading frame without classical termination. To investigate the mechanism of StopGo, we determined the cryo-EM structure of a mammalian ribosome positioned at the foot-and-mouth disease virus 2A (F2A) site. The structure shows how interactions between the F2A nascent chain (NC) and the ribosomal exit tunnel induce a conformational change in the peptidyl transferase center that precludes further translation elongation but instead pre-exposes the P-tRNA:F2A-NC ester bond for hydrolysis and NC release. Additionally, we bioinformatically characterized variation and host association across nearly 10,000 StopGo sequences identified in virus genomes. We expanded the canonical core motif to (D/G/C/N)(V/I)ExNPGP and identified additional rare but functional variants. We also revealed several distinct upstream motifs that we showed biochemically to be important for StopGo activity. Interestingly, although StopGo is known to be functionally active in plants, we found no evidence for natural utilization of StopGo by plant viruses. Overall, these findings provide valuable insights into a unique translation recoding mechanism, and lay foundations for further optimization of multigene expression in biotechnology. | |||||||||||||||
| 履歴 |
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構造の表示
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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_53976.map.gz | 155.9 MB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-53976-v30.xml emd-53976.xml | 152.3 KB 152.3 KB | 表示 表示 | EMDBヘッダ |
| FSC (解像度算出) | emd_53976_fsc.xml | 21.2 KB | 表示 | FSCデータファイル |
| 画像 | emd_53976.png | 158.1 KB | ||
| マスクデータ | emd_53976_msk_1.map | 824 MB | マスクマップ | |
| Filedesc metadata | emd-53976.cif.gz | 25.8 KB | ||
| その他 | emd_53976_additional_1.map.gz emd_53976_additional_2.map.gz emd_53976_half_map_1.map.gz emd_53976_half_map_2.map.gz | 664.2 MB 469.7 MB 668.7 MB 668.7 MB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-53976 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-53976 | HTTPS FTP |
-関連構造データ
| 関連構造データ | ![]() 9rhuMC 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 ( |
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| 類似構造データ | 類似検索 - 機能・相同性 F&H 検索 |
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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 |
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マップ
| ファイル | ダウンロード / ファイル: emd_53976.map.gz / 形式: CCP4 / 大きさ: 824 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| 注釈 | Sharpened, masked map (using B-factor of -10 and provided mask) | ||||||||||||||||||||||||||||||||||||
| 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: 0.702 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
-マスク #1
| ファイル | emd_53976_msk_1.map | ||||||||||||
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| 密度ヒストグラム |
-追加マップ: Unsharpened map from 3D refinement
| ファイル | emd_53976_additional_1.map | ||||||||||||
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| 注釈 | Unsharpened map from 3D refinement | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
-追加マップ: Map sharpened according to local resolution
| ファイル | emd_53976_additional_2.map | ||||||||||||
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| 注釈 | Map sharpened according to local resolution | ||||||||||||
| 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_53976_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_53976_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 stalled at the stop codon of a PGX mutant of ...
+超分子 #1: Rabbit 80S ribosome stalled at the stop codon of a PGX mutant of ...
+超分子 #2: 40S subunit
+超分子 #3: 60S subunit
+超分子 #4: P- and E-site tRNAs and nascent polypeptide chain
+超分子 #5: 40S subunit proteins
+超分子 #6: 18S rRNA
+超分子 #7: 60 subunit proteins
+超分子 #8: 5S, 5.8S, 28S rRNAs
+分子 #1: 60S ribosomal protein L34
+分子 #3: 60S ribosomal protein L6
+分子 #5: Small ribosomal subunit protein eS27
+分子 #6: 60S ribosomal protein L7
+分子 #8: Small ribosomal subunit protein eS28
+分子 #9: Large ribosomal subunit protein eL8
+分子 #11: Ubiquitin-ribosomal protein eS31 fusion protein
+分子 #12: 60S ribosomal protein L9
+分子 #13: Large ribosomal subunit protein uL2
+分子 #14: 40S ribosomal protein eS30
+分子 #15: 60S ribosomal protein L10
+分子 #16: Ribosomal protein L3
+分子 #17: eS26
+分子 #18: 60S ribosomal protein L11
+分子 #19: Large ribosomal subunit protein uL4
+分子 #20: Small ribosomal subunit protein RACK1
+分子 #21: Choriogonadotropin subunit beta variant 1,Genome polyprotein,Geno...
+分子 #22: Large ribosomal subunit protein uL18
+分子 #23: Small ribosomal subunit protein uS14
+分子 #24: Large ribosomal subunit protein eL13
+分子 #26: 60S ribosomal protein L14
+分子 #28: Ribosomal protein L15
+分子 #30: Large ribosomal subunit protein uL13
+分子 #31: Small ribosomal subunit protein uS2
+分子 #32: Large ribosomal subunit protein uL22
+分子 #33: 40S ribosomal protein S3a
+分子 #34: eL18
+分子 #35: 40S ribosomal protein S2
+分子 #36: Ribosomal protein L19
+分子 #37: Small ribosomal subunit protein uS3
+分子 #38: Large ribosomal subunit protein eL20
+分子 #39: 40S ribosomal protein S4
+分子 #40: 60S ribosomal protein L21
+分子 #41: Small ribosomal subunit protein uS7
+分子 #42: 60S ribosomal protein L22
+分子 #43: 40S ribosomal protein S6
+分子 #44: Ribosomal protein L23
+分子 #45: Small ribosomal subunit protein eS7
+分子 #46: Ribosomal protein L24
+分子 #47: 40S ribosomal protein S8
+分子 #48: Large ribosomal subunit protein uL23
+分子 #49: Small ribosomal subunit protein uS4
+分子 #50: Ribosomal protein L26
+分子 #51: eS10
+分子 #52: 60S ribosomal protein L27
+分子 #53: Small ribosomal subunit protein uS17
+分子 #54: 60S ribosomal protein L27a
+分子 #55: Small ribosomal subunit protein eS12
+分子 #56: 60S ribosomal protein L29
+分子 #57: Small ribosomal subunit protein uS15
+分子 #58: 60S ribosomal protein L30
+分子 #59: Small ribosomal subunit protein uS11
+分子 #60: 60S ribosomal protein L31
+分子 #61: Small ribosomal subunit protein uS19
+分子 #62: Ribosomal protein L32
+分子 #63: Small ribosomal subunit protein uS9
+分子 #64: 60S ribosomal protein L35a
+分子 #65: Small ribosomal subunit protein eS17
+分子 #66: Small ribosomal subunit protein uS13
+分子 #67: 60S ribosomal protein L35
+分子 #68: 40S ribosomal protein eS19
+分子 #69: Large ribosomal subunit protein eL36
+分子 #70: Small ribosomal subunit protein uS10
+分子 #71: Ribosomal protein L37
+分子 #72: Small ribosomal subunit protein eS21
+分子 #73: 60S ribosomal protein L38
+分子 #74: Small ribosomal subunit protein uS8
+分子 #75: 60S ribosomal protein L39-like
+分子 #76: 40S ribosomal protein S23
+分子 #77: Ubiquitin-ribosomal protein eL40 fusion protein
+分子 #78: 40S ribosomal protein S24
+分子 #79: Ribosomal protein L36a
+分子 #80: Small ribosomal subunit protein eS25
+分子 #81: 60S ribosomal protein L37a
+分子 #82: Small ribosomal subunit protein eS32
+分子 #83: [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B
+分子 #84: Large ribosomal subunit protein uL10
+分子 #85: 60S ribosomal protein L12
+分子 #86: Ribosomal protein uL1
+分子 #87: Eukaryotic peptide chain release factor subunit 1
+分子 #88: ATP binding cassette subfamily E member 1
+分子 #2: 18S rRNA
+分子 #4: 28S rRNA
+分子 #7: 5S rRNA
+分子 #10: 5.8S rRNA
+分子 #25: mRNA containing F2A sequence
+分子 #27: E-site tRNA-Pro
+分子 #29: P-site tRNA-Gly
+分子 #89: MAGNESIUM ION
+分子 #90: ZINC ION
+分子 #91: POTASSIUM ION
+分子 #92: SPERMIDINE
+分子 #93: GUANOSINE-5'-TRIPHOSPHATE
+分子 #94: IRON/SULFUR CLUSTER
-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 |
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試料調製
| 濃度 | 0.4 mg/mL | |||||||||||||||
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| 緩衝液 | pH: 7.4 構成要素:
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| グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / メッシュ: 300 / 支持フィルム - 材質: GRAPHENE OXIDE / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 45 sec. / 前処理 - 雰囲気: AIR | |||||||||||||||
| 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 |
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電子顕微鏡法
| 顕微鏡 | TFS KRIOS |
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| 撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 撮影したグリッド数: 2 / 実像数: 22565 / 平均露光時間: 1.2 sec. / 平均電子線量: 40.0 e/Å2 |
| 電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
| 電子光学系 | C2レンズ絞り径: 50.0 µm / 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / Cs: 2.7 mm / 最大 デフォーカス(公称値): 2.2 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 105000 |
| 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 |
ムービー
コントローラー
万見について




キーワード
Foot-and-mouth disease virus SAT 2 (ウイルス)
Homo sapiens (ヒト)
データ登録者
英国, European Union, 4件
引用



























Z (Sec.)
Y (Row.)
X (Col.)
































































解析
FIELD EMISSION GUN



