+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6swa | |||||||||||||||
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タイトル | Mus musculus brain neocortex ribosome 60S bound to Ebp1 | |||||||||||||||
要素 |
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キーワード | RIBOSOME (リボソーム) / 60S / EBP1 / neurodevelopment / neocortex / 80S / peptide tunnel exit | |||||||||||||||
機能・相同性 | 機能・相同性情報 5.8S rRNA binding / ヒドロキシル化 / translation at postsynapse / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit ...5.8S rRNA binding / ヒドロキシル化 / translation at postsynapse / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / : / selenocysteine insertion sequence binding / embryonic brain development / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / aminoacyl-tRNA synthetase multienzyme complex / negative regulation of formation of translation preinitiation complex / exit from mitosis / 90S preribosome assembly / optic nerve development / TORC2 complex binding / GAIT complex / retinal ganglion cell axon guidance / middle ear morphogenesis / peroxisome proliferator activated receptor binding / A band / regulation of G1 to G0 transition / alpha-beta T cell differentiation / protein-DNA complex disassembly / response to aldosterone / positive regulation of axonogenesis / G1 to G0 transition / homeostatic process / lung morphogenesis / cell-substrate adhesion / macrophage chemotaxis / growth factor binding / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / blastocyst development / protein-RNA complex assembly / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of axon extension / protein targeting / cellular response to interleukin-4 / translation regulator activity / cellular response to actinomycin D / ribonucleoprotein complex binding / 小胞体 / cytosolic ribosome / Neutrophil degranulation / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 骨化 / maturation of LSU-rRNA / cellular response to dexamethasone stimulus / ribosomal large subunit biogenesis / innate immune response in mucosa / skeletal system development / liver regeneration / positive regulation of cell differentiation / sensory perception of sound / 骨 / multicellular organism growth / transcription coactivator binding / cellular response to type II interferon / cytoplasmic ribonucleoprotein granule / rRNA processing / transcription corepressor activity / large ribosomal subunit / antimicrobial humoral immune response mediated by antimicrobial peptide / retina development in camera-type eye / presynapse / regulation of translation / heparin binding / 5S rRNA binding / cell body / large ribosomal subunit rRNA binding / fibroblast proliferation / antibacterial humoral response / postsynapse / response to ethanol / killing of cells of another organism / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / cytoplasmic translation / response to lipopolysaccharide / tRNA binding / nucleic acid binding / postsynaptic density / negative regulation of translation / protein stabilization / rRNA binding / リボソーム / structural constituent of ribosome / defense response to Gram-positive bacterium 類似検索 - 分子機能 | |||||||||||||||
生物種 | Mus musculus (ハツカネズミ) | |||||||||||||||
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: 3.1 Å | |||||||||||||||
データ登録者 | Kraushar, M.L. / Sprink, T. | |||||||||||||||
資金援助 | ドイツ, 4件
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引用 | ジャーナル: Mol Cell / 年: 2021 タイトル: Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit. 著者: Matthew L Kraushar / Ferdinand Krupp / Dermot Harnett / Paul Turko / Mateusz C Ambrozkiewicz / Thiemo Sprink / Koshi Imami / Manuel Günnigmann / Ulrike Zinnall / Carlos H Vieira-Vieira / ...著者: Matthew L Kraushar / Ferdinand Krupp / Dermot Harnett / Paul Turko / Mateusz C Ambrozkiewicz / Thiemo Sprink / Koshi Imami / Manuel Günnigmann / Ulrike Zinnall / Carlos H Vieira-Vieira / Theres Schaub / Agnieszka Münster-Wandowski / Jörg Bürger / Ekaterina Borisova / Hiroshi Yamamoto / Mladen-Roko Rasin / Uwe Ohler / Dieter Beule / Thorsten Mielke / Victor Tarabykin / Markus Landthaler / Günter Kramer / Imre Vida / Matthias Selbach / Christian M T Spahn / 要旨: Protein synthesis must be finely tuned in the developing nervous system as the final essential step of gene expression. This study investigates the architecture of ribosomes from the neocortex during ...Protein synthesis must be finely tuned in the developing nervous system as the final essential step of gene expression. This study investigates the architecture of ribosomes from the neocortex during neurogenesis, revealing Ebp1 as a high-occupancy 60S peptide tunnel exit (TE) factor during protein synthesis at near-atomic resolution by cryoelectron microscopy (cryo-EM). Ribosome profiling demonstrated Ebp1-60S binding is highest during start codon initiation and N-terminal peptide elongation, regulating ribosome occupancy of these codons. Membrane-targeting domains emerging from the 60S tunnel, which recruit SRP/Sec61 to the shared binding site, displace Ebp1. Ebp1 is particularly abundant in the early-born neural stem cell (NSC) lineage and regulates neuronal morphology. Ebp1 especially impacts the synthesis of membrane-targeted cell adhesion molecules (CAMs), measured by pulsed stable isotope labeling by amino acids in cell culture (pSILAC)/bioorthogonal noncanonical amino acid tagging (BONCAT) mass spectrometry (MS). Therefore, Ebp1 is a central component of protein synthesis, and the ribosome TE is a focal point of gene expression control in the molecular specification of neuronal morphology during development. | |||||||||||||||
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 | 6swa.cif.gz | 3 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6swa.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 6swa.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/sw/6swa ftp://data.pdbj.org/pub/pdb/validation_reports/sw/6swa | 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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1 |
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-要素
+60S ribosomal protein ... , 38種, 38分子 ABCDEFGHIJKLMNOPQRSTUVXYZabcde...
-Ribosomal protein ... , 4種, 4分子 Wjmn
#23: タンパク質 | 分子量: 15161.899 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q4FZH2 |
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#36: 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) Mus musculus (ハツカネズミ) / 参照: UniProt: Q505A8 |
#39: タンパク質 | 分子量: 12345.776 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q5M9P1 |
#40: タンパク質 | 分子量: 10168.153 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: Q4VAF2 |
-RNA鎖 , 3種, 3分子 qrs
#43: RNA鎖 | 分子量: 1170200.875 Da / 分子数: 1 / 由来タイプ: 天然 詳細: We used the Oryctolagus cuniculus sequence to model the Mus musculus 28S ribosomal RNA 由来: (天然) Mus musculus (ハツカネズミ) |
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#44: RNA鎖 | 分子量: 50449.812 Da / 分子数: 1 / 由来タイプ: 天然 詳細: We used the Oryctolagus cuniculus sequence to model the Mus musculus 5.8S ribosomal RNA 由来: (天然) Mus musculus (ハツカネズミ) / 参照: GenBank: 34447123 |
#45: RNA鎖 | 分子量: 38385.750 Da / 分子数: 1 / 由来タイプ: 天然 詳細: We used the Oryctolagus cuniculus sequence to model the Mus musculus 5S ribosomal RNA 由来: (天然) Mus musculus (ハツカネズミ) / 参照: GenBank: 1720429767 |
-タンパク質 , 1種, 1分子 t
#46: タンパク質 | 分子量: 39388.098 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) / 参照: UniProt: P50580 |
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-非ポリマー , 2種, 250分子
#47: 化合物 | ChemComp-MG / #48: 化合物 | |
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-詳細
研究の焦点であるリガンドがあるか | N |
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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: Mus musculus postnatal day 0 brain neocortex 80S ribosome bound to Ebp1 タイプ: RIBOSOME / Entity ID: #1-#46 / 由来: NATURAL | ||||||||||||||||||||||||||||||||||||||||
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分子量 | 値: 3.2 MDa / 実験値: NO | ||||||||||||||||||||||||||||||||||||||||
由来(天然) | 生物種: Mus musculus (ハツカネズミ) / 株: CD1 / 細胞内の位置: cytoplasm / 器官: brain / 組織: neocortex | ||||||||||||||||||||||||||||||||||||||||
緩衝液 | pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||
緩衝液成分 |
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試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||||||||||||||||||||||
試料支持 | グリッドの材料: COPPER / グリッドのサイズ: 100 divisions/in. / グリッドのタイプ: Quantifoil R3/3 | ||||||||||||||||||||||||||||||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK II / 凍結剤: ETHANE / 湿度: 100 % / 凍結前の試料温度: 277 K |
-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: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELDBright-field microscopy / 倍率(公称値): 31000 X / 最大 デフォーカス(公称値): 2500 nm / 最小 デフォーカス(公称値): 500 nm / Cs: 2.7 mm / アライメント法: COMA FREE |
試料ホルダ | 凍結剤: NITROGEN 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 平均露光時間: 20 sec. / 電子線照射量: 31.78 e/Å2 フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 実像数: 5379 |
電子光学装置 | エネルギーフィルター名称: GIF Quantum LS |
画像スキャン | 動画フレーム数/画像: 40 |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
粒子像の選択 | 選択した粒子像数: 208206 | |||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | |||||||||||||||||||||
3次元再構成 | 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 208206 / 対称性のタイプ: POINT |