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データを開く
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基本情報
登録情報 | ![]() | |||||||||
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タイトル | Mouse RPL39 integrated into the yeast 60S ribosomal subunit | |||||||||
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![]() | 60S ribosomal subunit / protein exit tunnel / RPL39 / RPL39L / RIBOSOME | |||||||||
機能・相同性 | ![]() 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 / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide ...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 / pre-mRNA 5'-splice site binding / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / response to cycloheximide / SRP-dependent cotranslational protein targeting to membrane / GTP hydrolysis and joining of the 60S ribosomal subunit / Formation of a pool of free 40S subunits / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of mRNA splicing, via spliceosome / L13a-mediated translational silencing of Ceruloplasmin expression / preribosome, large subunit precursor / translational elongation / ribosomal large subunit export from nucleus / protein-RNA complex assembly / regulation of translational fidelity / translational termination / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / translational initiation / macroautophagy / maintenance of translational fidelity / modification-dependent protein catabolic process / rRNA processing / protein tag activity / ribosome biogenesis / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / protein ubiquitination / structural constituent of ribosome / translation / response to antibiotic / mRNA binding / ubiquitin protein ligase binding / nucleolus / RNA binding / nucleus / metal ion binding / cytosol / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.15 Å | |||||||||
![]() | Rabl J / Banerjee A / Boehringer D / Zavolan M | |||||||||
資金援助 | ![]()
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![]() | ジャーナル: Acta Crystallogr D Struct Biol / 年: 2018 タイトル: Real-space refinement in PHENIX for cryo-EM and crystallography. 著者: Pavel V Afonine / Billy K Poon / Randy J Read / Oleg V Sobolev / Thomas C Terwilliger / Alexandre Urzhumtsev / Paul D Adams / ![]() ![]() ![]() 要旨: This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast ...This article describes the implementation of real-space refinement in the phenix.real_space_refine program from the PHENIX suite. The use of a simplified refinement target function enables very fast calculation, which in turn makes it possible to identify optimal data-restraint weights as part of routine refinements with little runtime cost. Refinement of atomic models against low-resolution data benefits from the inclusion of as much additional information as is available. In addition to standard restraints on covalent geometry, phenix.real_space_refine makes use of extra information such as secondary-structure and rotamer-specific restraints, as well as restraints or constraints on internal molecular symmetry. The re-refinement of 385 cryo-EM-derived models available in the Protein Data Bank at resolutions of 6 Å or better shows significant improvement of the models and of the fit of these models to the target maps. | |||||||||
履歴 |
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構造の表示
添付画像 |
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ダウンロードとリンク
-EMDBアーカイブ
マップデータ | ![]() | 775.2 MB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 61.6 KB 61.6 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 19.7 KB | 表示 | ![]() |
画像 | ![]() | 149.6 KB | ||
マスクデータ | ![]() | 824 MB | ![]() | |
Filedesc metadata | ![]() | 13.5 KB | ||
その他 | ![]() ![]() | 764 MB 763.9 MB | ||
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 | ![]() 8p8nMC ![]() 8p8mC M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
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類似構造データ | 類似検索 - 機能・相同性 ![]() |
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リンク
EMDBのページ | ![]() ![]() |
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「今月の分子」の関連する項目 |
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マップ
ファイル | ![]() | ||||||||||||||||||||
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ボクセルのサイズ | X=Y=Z: 0.84 Å | ||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
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-添付データ
-マスク #1
ファイル | ![]() | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #2
ファイル | emd_17550_half_map_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: #1
ファイル | emd_17550_half_map_2.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
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試料の構成要素
+全体 : Mouse RPL39 integrated into yeast 60S ribosomal subunit
+超分子 #1: Mouse RPL39 integrated into yeast 60S ribosomal subunit
+分子 #1: Large ribosomal subunit protein eL39
+分子 #2: 60S ribosomal protein L7-A
+分子 #3: 60S ribosomal protein L25
+分子 #4: 60S ribosomal protein L38
+分子 #6: 60S ribosomal protein L8-A
+分子 #7: 60S ribosomal protein L26-A
+分子 #8: Ubiquitin-60S ribosomal protein L40
+分子 #9: 60S ribosomal protein L13-A
+分子 #10: 60S ribosomal protein L9-A
+分子 #11: 60S ribosomal protein L27-A
+分子 #12: 60S ribosomal protein L42-A
+分子 #13: 60S ribosomal protein L14-A
+分子 #14: 60S ribosomal protein L10
+分子 #15: 60S ribosomal protein L28
+分子 #16: 60S ribosomal protein L43-A
+分子 #17: 60S ribosomal protein L15-A
+分子 #18: 60S ribosomal protein L11-A
+分子 #19: 60S ribosomal protein L29
+分子 #20: 60S ribosomal protein L17-A
+分子 #21: 60S ribosomal protein L16-A
+分子 #22: 60S ribosomal protein L18-A
+分子 #23: 60S ribosomal protein L30
+分子 #24: 60S ribosomal protein L19-A
+分子 #26: 60S ribosomal protein L20-A
+分子 #27: 60S ribosomal protein L31-A
+分子 #28: 60S ribosomal protein L21-A
+分子 #30: 60S ribosomal protein L22-A
+分子 #31: 60S ribosomal protein L32
+分子 #32: 60S ribosomal protein L23-A
+分子 #33: 60S ribosomal protein L2-A
+分子 #34: 60S ribosomal protein L24-A
+分子 #35: 60S ribosomal protein L33-A
+分子 #36: 60S ribosomal protein L3
+分子 #37: 60S ribosomal protein L34-A
+分子 #38: 60S ribosomal protein L4-A
+分子 #39: 60S ribosomal protein L35-A
+分子 #40: 60S ribosomal protein L5
+分子 #41: 60S ribosomal protein L36-A
+分子 #42: 60S ribosomal protein L6-A
+分子 #43: 60S ribosomal protein L37-A
+分子 #5: 25S rRNA
+分子 #25: 5.8S rRNA
+分子 #29: 5S rRNA
+分子 #44: MAGNESIUM ION
+分子 #45: CHLORIDE ION
+分子 #46: SPERMIDINE
+分子 #47: SPERMINE
+分子 #48: ZINC ION
+分子 #49: water
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
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![]() | 単粒子再構成法 |
試料の集合状態 | particle |
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試料調製
緩衝液 | pH: 7.6 |
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凍結 | 凍結剤: ETHANE-PROPANE |
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電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 45.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 照射モード: FLOOD BEAM / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.5 µm / 最小 デフォーカス(公称値): 1.0 µm |
実験機器 | ![]() モデル: Titan Krios / 画像提供: FEI Company |
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画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: OTHER |
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得られたモデル | ![]() PDB-8p8n: |