+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3jbp | ||||||
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タイトル | Cryo-electron microscopy reconstruction of the Plasmodium falciparum 80S ribosome bound to E-tRNA | ||||||
要素 |
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キーワード | RIBOSOME | ||||||
機能・相同性 | 機能・相同性情報 RMTs methylate histone arginines / Major pathway of rRNA processing in the nucleolus and cytosol / Protein methylation / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / Josephin domain DUBs / Metalloprotease DUBs ...RMTs methylate histone arginines / Major pathway of rRNA processing in the nucleolus and cytosol / Protein methylation / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / Translesion Synthesis by POLH / Translesion synthesis by POLK / Translesion synthesis by POLI / Josephin domain DUBs / Metalloprotease DUBs / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / ER Quality Control Compartment (ERQC) / Iron uptake and transport / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Translation initiation complex formation / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / GTP hydrolysis and joining of the 60S ribosomal subunit / Negative regulators of DDX58/IFIH1 signaling / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Aggrephagy / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / UCH proteinases / Ub-specific processing proteases / Neddylation / MAPK6/MAPK4 signaling / Antigen processing: Ubiquitination & Proteasome degradation / ABC-family proteins mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / protein-RNA complex assembly / 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) / maturation of LSU-rRNA / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosomal large subunit assembly / maturation of SSU-rRNA / small-subunit processome / maintenance of translational fidelity / mRNA 5'-UTR binding / modification-dependent protein catabolic process / rRNA processing / protein tag activity / large ribosomal subunit / ribosome biogenesis / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / ubiquitin-dependent protein catabolic process / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / nucleolus / mitochondrion / RNA binding / zinc ion binding / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | ||||||
生物種 | Plasmodium falciparum 3D7 (マラリア病原虫) | ||||||
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: 6.7 Å | ||||||
データ登録者 | Sun, M. / Li, W. / Blomqvist, K. / Das, S. / Hashem, Y. / Dvorin, J.D. / Frank, J. | ||||||
引用 | ジャーナル: Nucleic Acids Res / 年: 2015 タイトル: Dynamical features of the Plasmodium falciparum ribosome during translation. 著者: Ming Sun / Wen Li / Karin Blomqvist / Sanchaita Das / Yaser Hashem / Jeffrey D Dvorin / Joachim Frank / 要旨: Plasmodium falciparum, the mosquito-transmitted Apicomplexan parasite, causes the most severe form of human malaria. In the asexual blood-stage, the parasite resides within erythrocytes where it ...Plasmodium falciparum, the mosquito-transmitted Apicomplexan parasite, causes the most severe form of human malaria. In the asexual blood-stage, the parasite resides within erythrocytes where it proliferates, multiplies and finally spreads to new erythrocytes. Development of drugs targeting the ribosome, the site of protein synthesis, requires specific knowledge of its structure and work cycle, and, critically, the ways they differ from those in the human host. Here, we present five cryo-electron microscopy (cryo-EM) reconstructions of ribosomes purified from P. falciparum blood-stage schizonts at sub-nanometer resolution. Atomic models were built from these density maps by flexible fitting. Significantly, our study has taken advantage of new capabilities of cryo-EM, in visualizing several structures co-existing in the sample at once, at a resolution sufficient for building atomic models. We have discovered structural and dynamic features that differentiate the ribosomes of P. falciparum from those of mammalian system. Prompted by the absence of RACK1 on the ribosome in our and an earlier study we confirmed that RACK1 does not specifically co-purify with the 80S fraction in schizonts. More extensive studies, using cryo-EM methodology, of translation in the parasite will provide structural knowledge that may lead to development of novel anti-malarials. #1: ジャーナル: Elife / 年: 2014 タイトル: Cryo-EM structure of the Plasmodium falciparum 80S ribosome bound to the anti-protozoan drug emetine. 著者: Wilson Wong / Xiao-chen Bai / Alan Brown / Israel S Fernandez / Eric Hanssen / Melanie Condron / Yan Hong Tan / Jake Baum / Sjors H W Scheres / 要旨: Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as ...Malaria inflicts an enormous burden on global human health. The emergence of parasite resistance to front-line drugs has prompted a renewed focus on the repositioning of clinically approved drugs as potential anti-malarial therapies. Antibiotics that inhibit protein translation are promising candidates for repositioning. We have solved the cryo-EM structure of the cytoplasmic ribosome from the human malaria parasite, Plasmodium falciparum, in complex with emetine at 3.2 Å resolution. Emetine is an anti-protozoan drug used in the treatment of ameobiasis that also displays potent anti-malarial activity. Emetine interacts with the E-site of the ribosomal small subunit and shares a similar binding site with the antibiotic pactamycin, thereby delivering its therapeutic effect by blocking mRNA/tRNA translocation. As the first cryo-EM structure that visualizes an antibiotic bound to any ribosome at atomic resolution, this establishes cryo-EM as a powerful tool for screening and guiding the design of drugs that target parasite translation machinery. | ||||||
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 | 3jbp.cif.gz | 4.2 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3jbp.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 3jbp.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/jb/3jbp ftp://data.pdbj.org/pub/pdb/validation_reports/jb/3jbp | HTTPS FTP |
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-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
-RNA鎖 , 5種, 5分子 A7AAACAB
#1: RNA鎖 | 分子量: 517983.406 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Plasmodium falciparum 3D7 (マラリア病原虫) |
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#2: RNA鎖 | 分子量: 23774.059 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Plasmodium falciparum 3D7 (マラリア病原虫) |
#34: RNA鎖 | 分子量: 1027642.250 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Plasmodium falciparum 3D7 (マラリア病原虫) |
#35: RNA鎖 | 分子量: 48656.996 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Plasmodium falciparum 3D7 (マラリア病原虫) |
#36: RNA鎖 | 分子量: 38104.695 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Plasmodium falciparum 3D7 (マラリア病原虫) |
+40S ribosomal protein ... , 31種, 31分子 DEGIKMWROYZ123456BFHJLNPQSTUVXC
+60S ribosomal protein ... , 42種, 42分子 ALA1A2A4A6A7ANA8A9AaAbAdAeAfAPAhAiAIAJAcAKAMASAOAQARAWAYATAZ...
-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: Plasmodium falciparum 80S ribosome bound to E-tRNA / タイプ: RIBOSOME |
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緩衝液 | 名称: 10 mM HEPES potassium, 50 mM KOAc, 10 mM NH4Cl, 2 mM DTT, 5 mM Mg(OAc)2 pH: 7.5 詳細: 10 mM HEPES potassium, 50 mM KOAc, 10 mM NH4Cl, 2 mM DTT, 5 mM Mg(OAc)2 |
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: 300 mesh Copper/Molbydenum holey carton-coated Quantifoil R2/4 grid, containing an additional continuous thin layer of carbon |
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % 詳細: Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV). 手法: Blot for 4 seconds before plunging. |
-電子顕微鏡撮影
実験機器 | モデル: Tecnai Polara / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI POLARA 300 / 日付: 2013年10月13日 |
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): 23000 X / 倍率(補正後): 30120 X / 最大 デフォーカス(公称値): 3500 nm / 最小 デフォーカス(公称値): 1500 nm / Cs: 2.26 mm |
試料ホルダ | 資料ホルダタイプ: GATAN HELIUM |
撮影 | 電子線照射量: 25 e/Å2 / フィルム・検出器のモデル: GATAN K2 (4k x 4k) |
画像スキャン | デジタル画像の数: 5734 |
-解析
EMソフトウェア |
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CTF補正 | 詳細: Each micrograph | |||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||||||||
3次元再構成 | 解像度: 6.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 96732 / ピクセルサイズ(公称値): 1.66 Å / ピクセルサイズ(実測値): 1.66 Å / 対称性のタイプ: POINT | |||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT / 空間: REAL / 詳細: METHOD--Flexible fitting | |||||||||||||||||||||
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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