+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3jah | ||||||
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タイトル | Structure of a mammalian ribosomal termination complex with ABCE1, eRF1(AAQ), and the UAG stop codon | ||||||
要素 |
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キーワード | RIBOSOME / termination / eRF1 / ABCE1 | ||||||
機能・相同性 | 機能・相同性情報 translation termination factor activity / cytoplasmic translational termination / translation release factor complex / translation release factor activity / regulation of translational termination / ribosomal subunit / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity ...translation termination factor activity / cytoplasmic translational termination / translation release factor complex / translation release factor activity / regulation of translational termination / ribosomal subunit / translation release factor activity, codon specific / protein methylation / sequence-specific mRNA binding / aminoacyl-tRNA hydrolase activity / regulation of G1 to G0 transition / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / 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 / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / Protein hydroxylation / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / ribosomal small subunit binding / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / 90S preribosome / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / T cell proliferation involved in immune response / erythrocyte development / cellular response to actinomycin D / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal subunit export from nucleus / ribosomal small subunit export from nucleus / translation regulator activity / translational termination / 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 / maturation of LSU-rRNA / cytosolic ribosome / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / positive regulation of translation / small-subunit processome / translational initiation / protein kinase C binding / positive regulation of apoptotic signaling pathway / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / spindle / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / ribosomal small subunit biogenesis / rhythmic process / positive regulation of canonical Wnt signaling pathway / small ribosomal subunit rRNA binding / ribosome biogenesis / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / T cell differentiation in thymus / large ribosomal subunit rRNA binding / cell body / 5S rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / cytosolic large ribosomal subunit / tRNA binding / mitochondrial inner membrane / cell differentiation / postsynaptic density / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / iron ion binding / positive regulation of apoptotic process 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Oryctolagus cuniculus (ウサギ) | ||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.45 Å | ||||||
データ登録者 | Brown, A. / Shao, S. / Murray, J. / Hegde, R.S. / Ramakrishnan, V. | ||||||
引用 | ジャーナル: Nature / 年: 2015 タイトル: Structural basis for stop codon recognition in eukaryotes. 著者: Alan Brown / Sichen Shao / Jason Murray / Ramanujan S Hegde / V Ramakrishnan / 要旨: Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal ...Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UAA, UAG or UGA. Release factors recognize stop codons in the ribosomal A-site to mediate release of the nascent chain and recycling of the ribosome. Bacteria decode stop codons using two separate release factors with differing specificities for the second and third bases. By contrast, eukaryotes rely on an evolutionarily unrelated omnipotent release factor (eRF1) to recognize all three stop codons. The molecular basis of eRF1 discrimination for stop codons over sense codons is not known. Here we present cryo-electron microscopy (cryo-EM) structures at 3.5-3.8 Å resolution of mammalian ribosomal complexes containing eRF1 interacting with each of the three stop codons in the A-site. Binding of eRF1 flips nucleotide A1825 of 18S ribosomal RNA so that it stacks on the second and third stop codon bases. This configuration pulls the fourth position base into the A-site, where it is stabilized by stacking against G626 of 18S rRNA. Thus, eRF1 exploits two rRNA nucleotides also used during transfer RNA selection to drive messenger RNA compaction. In this compacted mRNA conformation, stop codons are favoured by a hydrogen-bonding network formed between rRNA and essential eRF1 residues that constrains the identity of the bases. These results provide a molecular framework for eukaryotic stop codon recognition and have implications for future studies on the mechanisms of canonical and premature translation termination. | ||||||
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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 3jah.cif.gz | 5.6 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3jah.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 3jah.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 3jah_validation.pdf.gz | 1.5 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3jah_full_validation.pdf.gz | 1.8 MB | 表示 | |
XML形式データ | 3jah_validation.xml.gz | 366 KB | 表示 | |
CIF形式データ | 3jah_validation.cif.gz | 637.7 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ja/3jah ftp://data.pdbj.org/pub/pdb/validation_reports/ja/3jah | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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-要素
+タンパク質 , 77種, 77分子 ABCDEFGHIJLMNOPQRSTUVWXYZabcde...
-タンパク質・ペプチド , 3種, 3分子 ln1
#37: タンパク質・ペプチド | 分子量: 6295.562 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / Cell: reticulocyte lysate / 参照: UniProt: G1SYU7 |
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#39: タンパク質・ペプチド | 分子量: 3213.075 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / Cell: reticulocyte lysate / 参照: UniProt: A0A087WNH4 |
#45: タンパク質・ペプチド | 分子量: 1788.032 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / Cell: reticulocyte lysate |
-RNA鎖 , 7種, 7分子 235789hh
#46: RNA鎖 | 分子量: 24436.551 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / Cell: reticulocyte lysate |
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#47: RNA鎖 | 分子量: 24102.275 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / Cell: reticulocyte lysate |
#48: RNA鎖 | 分子量: 1186579.500 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / Cell: reticulocyte lysate |
#49: RNA鎖 | 分子量: 38691.914 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / Cell: reticulocyte lysate |
#50: RNA鎖 | 分子量: 50143.648 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / Cell: reticulocyte lysate |
#51: RNA鎖 | 分子量: 554751.312 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / Cell: reticulocyte lysate |
#85: RNA鎖 | 分子量: 3837.328 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / Cell: reticulocyte lysate |
-非ポリマー , 4種, 207分子
#88: 化合物 | ChemComp-MG / #89: 化合物 | ChemComp-ZN / #90: 化合物 | #91: 化合物 | |
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-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 |
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緩衝液 | 名称: 50 mM HEPES, 100 mM potassium acetate, 5 mM magnesium acetate, 1 mM DTT pH: 7.4 詳細: 50 mM HEPES, 100 mM potassium acetate, 5 mM magnesium acetate, 1 mM DTT | ||||||||||||||||||||||||||||||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||||||||||||
試料支持 | 詳細: Quantifoil R2/2 400 mesh Cu grid with thin continuous carbon support, glow discharged | ||||||||||||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK III / 凍結剤: ETHANE / 湿度: 100 % 詳細: After 30 second wait time, blot for 3 seconds before plunging into liquid ethane (FEI VITROBOT MARK III). 手法: After 30 second wait time, blot for 3 seconds before plunging |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS / 日付: 2015年2月25日 / 詳細: Automated data acquisition using EPU (FEI) |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 59000 X / 倍率(補正後): 104478 X / 最大 デフォーカス(公称値): 3600 nm / 最小 デフォーカス(公称値): 1700 nm / Cs: 2.7 mm |
試料ホルダ | 資料ホルダタイプ: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 電子線照射量: 30 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
画像スキャン | デジタル画像の数: 1601 |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
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対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||
3次元再構成 | 解像度: 3.45 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 20515 / ピクセルサイズ(公称値): 1.34 Å / ピクセルサイズ(実測値): 1.34 Å / 対称性のタイプ: POINT | ||||||||||||||||||||
原子モデル構築 |
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原子モデル構築 |
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精密化ステップ | サイクル: LAST
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