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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 6g4w | |||||||||||||||
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タイトル | Cryo-EM structure of a late human pre-40S ribosomal subunit - State A | |||||||||||||||
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![]() | RIBOSOME / 40S / pre-40S / ribosome biogenesis | |||||||||||||||
機能・相同性 | ![]() peptidyl-glutamine methylation / regulation of protein localization to nucleolus / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / tRNA modification in the nucleus and cytosol / Methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / protein methyltransferase activity ...peptidyl-glutamine methylation / regulation of protein localization to nucleolus / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / tRNA modification in the nucleus and cytosol / Methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / protein methyltransferase activity / positive regulation of rRNA processing / tRNA methylation / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / : / negative regulation of RNA splicing / neural crest cell differentiation / rRNA methylation / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / U3 snoRNA binding / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / preribosome, small subunit precursor / Translation initiation complex formation / mammalian oogenesis stage / snoRNA binding / activation-induced cell death of T cells / fibroblast growth factor binding / Protein hydroxylation / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / monocyte chemotaxis / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / TOR signaling / T cell proliferation involved in immune response / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity / ribosomal small subunit export from nucleus / negative regulation of ubiquitin-dependent protein catabolic process / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / translation regulator activity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / positive regulation of cell cycle / cytosolic ribosome / stress granule assembly / Mitotic Prometaphase / rough endoplasmic reticulum / EML4 and NUDC in mitotic spindle formation / gastrulation / MDM2/MDM4 family protein binding / transcription initiation-coupled chromatin remodeling / translation initiation factor binding / Resolution of Sister Chromatid Cohesion / 90S preribosome / 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの / erythrocyte differentiation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / innate immune response in mucosa / stem cell proliferation / translational initiation / cellular response to leukemia inhibitory factor / methyltransferase activity / maturation of SSU-rRNA / neural tube closure / mRNA 3'-UTR binding / positive regulation of translation / RHO GTPases Activate Formins / liver regeneration / small-subunit processome / maintenance of translational fidelity / response to virus / placenta development / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / G1/S transition of mitotic cell cycle / osteoblast differentiation / rRNA processing / Separation of Sister Chromatids / antimicrobial humoral immune response mediated by antimicrobial peptide / ribosome biogenesis / apical part of cell 類似検索 - 分子機能 | |||||||||||||||
生物種 | ![]() | |||||||||||||||
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: 4.5 Å | |||||||||||||||
![]() | Ameismeier, M. / Cheng, J. / Berninghausen, O. / Beckmann, R. | |||||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Visualizing late states of human 40S ribosomal subunit maturation. 著者: Michael Ameismeier / Jingdong Cheng / Otto Berninghausen / Roland Beckmann / ![]() 要旨: The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high- ...The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available only from fungi. Here we present cryo-electron microscopy structures of late-stage human 40S assembly intermediates, representing one state reconstituted in vitro and five native states that range from nuclear to late cytoplasmic. The earliest particles reveal the position of the biogenesis factor RRP12 and distinct immature rRNA conformations that accompany the formation of the 40S subunit head. Molecular models of the late-acting assembly factors TSR1, RIOK1, RIOK2, ENP1, LTV1, PNO1 and NOB1 provide mechanistic details that underlie their contribution to a sequential 40S subunit assembly. The NOB1 architecture displays an inactive nuclease conformation that requires rearrangement of the PNO1-bound 3' rRNA, thereby coordinating the final rRNA folding steps with site 3 cleavage. | |||||||||||||||
履歴 |
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構造の表示
ムービー |
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構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 1.2 MB | 表示 | ![]() |
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PDB形式 | ![]() | 848.9 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 964.8 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1015.5 KB | 表示 | |
XML形式データ | ![]() | 128.4 KB | 表示 | |
CIF形式データ | ![]() | 232.5 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 4349MC ![]() 4337C ![]() 4348C ![]() 4350C ![]() 4351C ![]() 4352C ![]() 4353C ![]() 6g18C ![]() 6g4sC ![]() 6g51C ![]() 6g53C ![]() 6g5hC ![]() 6g5iC M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 ( |
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類似構造データ |
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リンク
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集合体
登録構造単位 | ![]()
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要素
-RNA鎖 , 1種, 1分子 2
#1: RNA鎖 | 分子量: 607057.688 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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+40S ribosomal protein ... , 22種, 22分子 RbBcEeFHGZYXWTSQPONLJI
-タンパク質 , 6種, 6分子 xwusrq
#13: タンパク質 | 分子量: 27970.355 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#15: タンパク質 | 分子量: 49673.258 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#17: タンパク質 | 分子量: 91951.188 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#28: タンパク質 | 分子量: 68101.625 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#29: タンパク質 | 分子量: 14215.359 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
#30: タンパク質 | 分子量: 31925.428 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() 参照: UniProt: O43709, 転移酵素; 一炭素原子の基を移すもの; メチル基を移すもの |
-タンパク質・ペプチド , 2種, 2分子 tk
#18: タンパク質・ペプチド | 分子量: 2054.328 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
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#31: タンパク質・ペプチド | 分子量: 1368.494 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) ![]() |
-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 |
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試料調製
構成要素 | 名称: Cryo-EM structure of a late human pre-40S ribosomal subunit - State A タイプ: RIBOSOME / Entity ID: all / 由来: NATURAL |
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分子量 | 実験値: NO |
由来(天然) | 生物種: ![]() |
緩衝液 | pH: 7.6 |
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 |
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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: ![]() |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 2.5 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
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解析
CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3次元再構成 | 解像度: 4.5 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 52414 / 対称性のタイプ: POINT |