EMDB/PDB/SASBDBから引用されている文献のデータベース

キーワード
構造解析手法	All X線回折 NMR 電子顕微鏡小角散乱中性子線回折線維回折粉末回折赤外分光 EPR FRET 理論モデルハイブリッド
著者・登録者
ジャーナル
IF	>30 >20 >10 >5 all

タイトル	The missing part: the Archaeoglobus fulgidus Argonaute forms a functional heterodimer with an N-L1-L2 domain protein.
ジャーナル・号・ページ	Nucleic Acids Res, Vol. 52, Issue 5, Page 2530-2545, Year 2024
掲載日	2024年3月21日
著者	Elena Manakova / Edvardas Golovinas / Reda Pocevičiūtė / Giedrius Sasnauskas / Arunas Silanskas / Danielis Rutkauskas / Marija Jankunec / Evelina Zagorskaitė / Edvinas Jurgelaitis / Algirdas Grybauskas / Česlovas Venclovas / Mindaugas Zaremba
PubMed 要旨	Argonaute (Ago) proteins are present in all three domains of life (bacteria, archaea and eukaryotes). They use small (15-30 nucleotides) oligonucleotide guides to bind complementary nucleic acid ...Argonaute (Ago) proteins are present in all three domains of life (bacteria, archaea and eukaryotes). They use small (15-30 nucleotides) oligonucleotide guides to bind complementary nucleic acid targets and are responsible for gene expression regulation, mobile genome element silencing, and defence against viruses or plasmids. According to their domain organization, Agos are divided into long and short Agos. Long Agos found in prokaryotes (long-A and long-B pAgos) and eukaryotes (eAgos) comprise four major functional domains (N, PAZ, MID and PIWI) and two structural linker domains L1 and L2. The majority (∼60%) of pAgos are short pAgos, containing only the MID and inactive PIWI domains. Here we focus on the prokaryotic Argonaute AfAgo from Archaeoglobus fulgidus DSM4304. Although phylogenetically classified as a long-B pAgo, AfAgo contains only MID and catalytically inactive PIWI domains, akin to short pAgos. We show that AfAgo forms a heterodimeric complex with a protein encoded upstream in the same operon, which is a structural equivalent of the N-L1-L2 domains of long pAgos. This complex, structurally equivalent to a long PAZ-less pAgo, outperforms standalone AfAgo in guide RNA-mediated target DNA binding. Our findings provide a missing piece to one of the first and the most studied pAgos.
リンク	Nucleic Acids Res / PubMed:38197228 / PubMed Central
手法	EM (単粒子) / X線回折
解像度	1.4 - 3.43 Å
構造データ	17973 8pvv EMDB-17973, PDB-8pvv: Archaeoglobus fulgidus AfAgo complex with AfAgo-N protein (fAfAgo) bound with 30 nt RNA guide and 51 nt DNA target 手法: EM (単粒子) / 解像度: 2.81 Å 18386 8qg0 EMDB-18386, PDB-8qg0: Archaeoglobus fulgidus AfAgo complex with AfAgo-N protein (fAfAgo) bound with 17 nt RNA guide and 17 nt DNA target 手法: EM (単粒子) / 解像度: 3.43 Å PDB-8ok9: Heterodimeric complex of Archaeoglobus fulgidus Argonaute protein Af1318 (AfAgo) with DNA and AfAgo-N protein containing N-L1-L2 domains 手法: X-RAY DIFFRACTION / 解像度: 2.5 Å PDB-8old: Crystal structure of Archaeoglobus fulgidus AfAgo-N protein representing N-L1-L2 domains 手法: X-RAY DIFFRACTION / 解像度: 1.85 Å PDB-8olj: Crystal structure of Archaeoglobus fulgidus AfAgo-N protein representing N-L1-L2 domains 手法: X-RAY DIFFRACTION / 解像度: 1.4 Å
化合物	ChemComp-MG: Unknown entry / マグネシウムジカチオン ChemComp-ACY: ACETIC ACID / 酢酸 / 酢酸 ChemComp-EDO: 1,2-ETHANEDIOL / エチレングリコ-ル / エチレングリコール ChemComp-PEG: DI(HYDROXYETHYL)ETHER / ジエチレングリコ-ル / ジエチレングリコール ChemComp-HOH: WATER / 水 ChemComp-CAC: CACODYLATE ION / ジメチルアルシン酸アニオン / カコジル酸 ChemComp-CL: Unknown entry / クロリド / 塩化物 ChemComp-MPD: (4S)-2-METHYL-2,4-PENTANEDIOL / (S)-2-メチル-2,4-ペンタンジオ-ル / 沈殿剤YM / 2-Methyl-2,4-pentanediol ChemComp-NA: Unknown entry / ナトリウムカチオン ChemComp-GOL: GLYCEROL / グリセロ-ル / グリセリン ChemComp-IPA: ISOPROPYL ALCOHOL / 2-プロパノ-ル / alkaloidYM / 2-プロパノール ChemComp-K: Unknown entry / カリウムカチオン ChemComp-TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / トリス(ヒドロキシメチル)メチルアンモニウム / pH緩衝剤*YM / トリスヒドロキシメチルアミノメタン
由来	archaeoglobus fulgidus (アルカエオグロブス属) archaeoglobus fulgidus dsm 8774 (アルカエオグロブス属) escherichia coli (大腸菌) archaeoglobus fulgidus dsm 4304 (アルカエオグロブス属)
キーワード	RNA BINDING PROTEIN (RNA結合タンパク質) / Protein-nucleic acid interactions / Argonaute (アルゴノート (タンパク質)) / pAgo / guide and target specificity / PROTEIN BINDING (タンパク質) / DNA BINDING PROTEIN (DNA結合タンパク質) / PIWI DOMAIN / PROTEIN-DNA COMPLEX (デオキシリボ核酸)