+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6d9j | ||||||
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タイトル | Mammalian 80S ribosome with a double translocated CrPV-IRES, P-sitetRNA and eRF1. | ||||||
要素 |
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キーワード | RIBOSOME / mammalian / CrPV IRES | ||||||
機能・相同性 | 機能・相同性情報 Synthesis of diphthamide-EEF2 / ribosomal subunit / aggresome / 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 ...Synthesis of diphthamide-EEF2 / ribosomal subunit / aggresome / 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 / Uptake and function of diphtheria toxin / retinal ganglion cell axon guidance / mammalian oogenesis stage / G1 to G0 transition / activation-induced cell death of T cells / Peptide chain elongation / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / translational elongation / 90S preribosome / TOR signaling / T cell proliferation involved in immune response / hematopoietic progenitor cell differentiation / erythrocyte development / translation elongation factor activity / Protein methylation / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal small subunit export from nucleus / translation regulator activity / rough endoplasmic reticulum / 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 / 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 / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / ribosomal small subunit biogenesis / rhythmic process / positive regulation of canonical Wnt signaling pathway / small ribosomal subunit rRNA 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 / ribosome biogenesis / ribosome binding / glucose homeostasis / regulation of translation / retina development in camera-type eye / 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 / secretory granule lumen / cytoplasmic translation / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / ficolin-1-rich granule lumen / killing of cells of another organism / tRNA binding / mitochondrial inner membrane / cell differentiation / postsynaptic density / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / cadherin binding / positive regulation of apoptotic process / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Oryctolagus cuniculus (ウサギ) Escherichia coli (大腸菌) Cricket paralysis virus (ウイルス) | ||||||
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: 3.2 Å | ||||||
データ登録者 | Pisareva, V.P. / Pisarev, A.V. / Fernandez, I.S. | ||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Elife / 年: 2018 タイトル: Dual tRNA mimicry in the Cricket Paralysis Virus IRES uncovers an unexpected similarity with the Hepatitis C Virus IRES. 著者: Vera P Pisareva / Andrey V Pisarev / Israel S Fernández / 要旨: Co-opting the cellular machinery for protein production is a compulsory requirement for viruses. The Cricket Paralysis Virus employs an Internal Ribosomal Entry Site (CrPV-IRES) to express its ...Co-opting the cellular machinery for protein production is a compulsory requirement for viruses. The Cricket Paralysis Virus employs an Internal Ribosomal Entry Site (CrPV-IRES) to express its structural genes in the late stage of infection. Ribosome hijacking is achieved by a sophisticated use of molecular mimicry to tRNA and mRNA, employed to manipulate intrinsically dynamic components of the ribosome. Binding and translocation through the ribosome is required for this IRES to initiate translation. We report two structures, solved by single particle electron cryo-microscopy (cryoEM), of a double translocated CrPV-IRES with aminoacyl-tRNA in the peptidyl site (P site) of the ribosome. CrPV-IRES adopts a previously unseen conformation, mimicking the acceptor stem of a canonical E site tRNA. The structures suggest a mechanism for the positioning of the first aminoacyl-tRNA shared with the distantly related Hepatitis C Virus IRES. | ||||||
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 | 6d9j.cif.gz | 5 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6d9j.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 6d9j.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 | 6d9j_validation.pdf.gz | 1.7 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6d9j_full_validation.pdf.gz | 1.9 MB | 表示 | |
XML形式データ | 6d9j_validation.xml.gz | 368.7 KB | 表示 | |
CIF形式データ | 6d9j_validation.cif.gz | 639.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/d9/6d9j ftp://data.pdbj.org/pub/pdb/validation_reports/d9/6d9j | 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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1 |
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-要素
+タンパク質 , 78種, 78分子 ABCDEFGHIJLMNOPQRSTUVWXYZabcde...
-タンパク質・ペプチド , 1種, 1分子 n
#39: タンパク質・ペプチド | 分子量: 3473.451 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) |
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-RNA鎖 , 6種, 6分子 578234
#45: RNA鎖 | 分子量: 1164731.875 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) |
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#46: RNA鎖 | 分子量: 38385.750 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) / 参照: REF: 1304938343 |
#47: RNA鎖 | 分子量: 48545.672 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) |
#49: RNA鎖 | 分子量: 547733.062 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Oryctolagus cuniculus (ウサギ) |
#83: RNA鎖 | 分子量: 28094.645 Da / 分子数: 1 / 由来タイプ: 合成 詳細: RNA was prepared by in vitro transcription with T7 RNA polymerase 由来: (合成) Escherichia coli (大腸菌) / 参照: GenBank: 1370526512 |
#85: RNA鎖 | 分子量: 60789.762 Da / 分子数: 1 / 由来タイプ: 合成 詳細: RNA was prepared by in vitro transcription with T7 RNA polymerase 由来: (合成) Cricket paralysis virus (ウイルス) / 参照: GenBank: 8895506 |
-非ポリマー , 2種, 6分子
#86: 化合物 | ChemComp-ZN / #87: 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 | 名称: Mammalian 80S ribosome in complex with translocated CrPV IRES, P-site tRNA and eEF2 タイプ: RIBOSOME 詳細: Mammalian 80S ribosome in complex with translocated CrPV IRES, P-site tRNA and eRF1 Entity ID: #1-#85 / 由来: NATURAL |
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分子量 | 値: 5 MDa / 実験値: NO |
由来(天然) | 生物種: Oryctolagus cuniculus (ウサギ) |
緩衝液 | pH: 7.4 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-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 |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 64 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | タイプ: NONE | ||||||||||||
3次元再構成 | 解像度: 3.2 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 75654 / 対称性のタイプ: POINT |