+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 4v6w | |||||||||
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タイトル | Structure of the D. melanogaster 80S ribosome | |||||||||
要素 |
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キーワード | RIBOSOME / eukarya / eukaryotic / ribosomal / 80S / RNA / protein synthesis / mass spectrometry | |||||||||
機能・相同性 | 機能・相同性情報 Peptide chain elongation / Synthesis of diphthamide-EEF2 / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / Activation of the IkappaB kinase complex, KEY:IRD5 dimer:KEY / NF-kB is activated and signals survival / Downregulation of TGF-beta receptor signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Regulation of innate immune responses to cytosolic DNA ...Peptide chain elongation / Synthesis of diphthamide-EEF2 / APC/C:Cdc20 mediated degradation of Cyclin B / SCF-beta-TrCP mediated degradation of Emi1 / SRP-dependent cotranslational protein targeting to membrane / Activation of the IkappaB kinase complex, KEY:IRD5 dimer:KEY / NF-kB is activated and signals survival / Downregulation of TGF-beta receptor signaling / SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription / Regulation of innate immune responses to cytosolic DNA / Gap-filling DNA repair synthesis and ligation in TC-NER / Major pathway of rRNA processing in the nucleolus and cytosol / Regulation of TP53 Degradation / Cyclin D associated events in G1 / Formation of a pool of free 40S subunits / Formation of the ternary complex, and subsequently, the 43S complex / GTP hydrolysis and joining of the 60S ribosomal subunit / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Protein methylation / ER Quality Control Compartment (ERQC) / Iron uptake and transport / RAS processing / Pexophagy / Regulation of BACH1 activity / Regulation of pyruvate metabolism / polytene chromosome chromocenter / Translesion synthesis by REV1 / Downregulation of SMAD2/3:SMAD4 transcriptional activity / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Translesion synthesis by POLK / Translesion synthesis by POLI / Ovarian tumor domain proteases / Formation of Incision Complex in GG-NER / Formation of TC-NER Pre-Incision Complex / Regulation of expression of SLITs and ROBOs / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Translesion Synthesis by POLH / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / APC-Cdc20 mediated degradation of Nek2A / SCF(Skp2)-mediated degradation of p27/p21 / Degradation of beta-catenin by the destruction complex / Ubiquitination and degradation of phosphorylated ARM / Separation of Sister Chromatids / Degradation of AXIN / Degradation of DVL / Regulation of TNFR1 signaling / Dectin-1 mediated noncanonical NF-kB signaling / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / NIK-->noncanonical NF-kB signaling / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RUNX2 expression and activity / Regulation of RUNX3 expression and activity / Peroxisomal protein import / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Recognition of DNA damage by PCNA-containing replication complex / Downregulation of ERBB2:ERBB3 signaling / Activated NOTCH1 Transmits Signal to the Nucleus / Nuclear CI is degraded / ABC-family proteins mediated transport / TAK1-dependent IKK and NF-kappa-B activation / activated TAK1 mediates p38 MAPK activation / PINK1-PRKN Mediated Mitophagy / Hedgehog ligand biogenesis / Josephin domain DUBs / Dual Incision in GG-NER / Dual incision in TC-NER / Downregulation of ERBB2 signaling / VLDLR internalisation and degradation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK1 recruits IKK complex / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / KEAP1-NFE2L2 pathway / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Ubiquitination and proteolysis of phosphorylated CI / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Spry regulation of FGF signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / Interleukin-1 signaling / Regulation of signaling by CBL / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / polytene chromosome puff / pupariation / Downregulation of ERBB4 signaling / Degradation of PER / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome 類似検索 - 分子機能 | |||||||||
生物種 | Drosophila melanogaster (キイロショウジョウバエ) | |||||||||
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 Å | |||||||||
データ登録者 | Anger, A.M. / Armache, J.-P. / Berninghausen, O. / Habeck, M. / Subklewe, M. / Wilson, D.N. / Beckmann, R. | |||||||||
引用 | ジャーナル: Nature / 年: 2013 タイトル: Structures of the human and Drosophila 80S ribosome. 著者: Andreas M Anger / Jean-Paul Armache / Otto Berninghausen / Michael Habeck / Marion Subklewe / Daniel N Wilson / Roland Beckmann / 要旨: Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex ...Protein synthesis in all cells is carried out by macromolecular machines called ribosomes. Although the structures of prokaryotic, yeast and protist ribosomes have been determined, the more complex molecular architecture of metazoan 80S ribosomes has so far remained elusive. Here we present structures of Drosophila melanogaster and Homo sapiens 80S ribosomes in complex with the translation factor eEF2, E-site transfer RNA and Stm1-like proteins, based on high-resolution cryo-electron-microscopy density maps. These structures not only illustrate the co-evolution of metazoan-specific ribosomal RNA with ribosomal proteins but also reveal the presence of two additional structural layers in metazoan ribosomes, a well-ordered inner layer covered by a flexible RNA outer layer. The human and Drosophila ribosome structures will provide the basis for more detailed structural, biochemical and genetic experiments. | |||||||||
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 | 4v6w.cif.gz | 5.2 MB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb4v6w.ent.gz | 表示 | PDB形式 | |
PDBx/mmJSON形式 | 4v6w.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
文書・要旨 | 4v6w_validation.pdf.gz | 1.9 MB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 4v6w_full_validation.pdf.gz | 3.6 MB | 表示 | |
XML形式データ | 4v6w_validation.xml.gz | 538 KB | 表示 | |
CIF形式データ | 4v6w_validation.cif.gz | 862.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/v6/4v6w ftp://data.pdbj.org/pub/pdb/validation_reports/v6/4v6w | HTTPS FTP |
-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
-タンパク質 , 4種, 4分子 AzAgAhCq
#1: タンパク質 | 分子量: 94585.961 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: P13060 |
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#2: タンパク質 | 分子量: 35661.934 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: O18640 |
#35: タンパク質 | 分子量: 13542.481 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: Q9VBX3 |
#39: タンパク質 | 分子量: 24401.459 Da / 分子数: 1 / Fragment: SEE REMARK 999 / 由来タイプ: 天然 由来: (天然) Drosophila melanogaster (キイロショウジョウバエ) 参照: UniProt: P05388*PLUS |
+40S ribosomal protein ... , 32種, 32分子 AUAKAOAXAMASAdANALARAPATABAAAVAYAZAaAbAcADAeAfAJAEACAGAFAHAWAIAQ
-RNA鎖 , 6種, 6分子 B2BCA5A9A7A8
#36: RNA鎖 | 分子量: 641830.375 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Drosophila melanogaster (キイロショウジョウバエ) 参照: GenBank: M21017 |
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#37: RNA鎖 | 分子量: 24249.477 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Drosophila melanogaster (キイロショウジョウバエ) 参照: GenBank: K00325 |
#83: RNA鎖 | 分子量: 1277668.500 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Drosophila melanogaster (キイロショウジョウバエ) 参照: GenBank: M21017 |
#84: RNA鎖 | 分子量: 9665.705 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Drosophila melanogaster (キイロショウジョウバエ) 参照: GenBank: M21017 |
#85: RNA鎖 | 分子量: 38627.906 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Drosophila melanogaster (キイロショウジョウバエ) 参照: GenBank: M25016 |
#86: RNA鎖 | 分子量: 39616.551 Da / 分子数: 1 / 由来タイプ: 天然 由来: (天然) Drosophila melanogaster (キイロショウジョウバエ) 参照: GenBank: M21017 |
+60S ribosomal protein ... , 44種, 44分子 CzCKCOCLCVCMCaCNCICDCQCRCACSCTCPCUCXCYCWCZCrChCbCBCFCcCdCeCf...
-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 |
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分子量 | 値: 4 MDa / 実験値: NO | ||||||||||||
緩衝液 | pH: 7.5 | ||||||||||||
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||
急速凍結 | 装置: FEI VITROBOT MARK IV / 凍結剤: ETHANE / 湿度: 100 % 詳細: Blot for 3 seconds using two pieces of filter paper, then plunge into liquid ethane (FEI VITROBOT MARK IV). |
-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 / 日付: 2011年3月10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): 90000 X / 倍率(補正後): 90000 X / 最大 デフォーカス(公称値): 4000 nm / 最小 デフォーカス(公称値): 1000 nm / Cs: 2.7 mm |
試料ホルダ | 試料ホルダーモデル: GATAN LIQUID NITROGEN / 資料ホルダタイプ: GATAN LIQUID NITROGEN |
撮影 | 電子線照射量: 20 e/Å2 / フィルム・検出器のモデル: FEI EAGLE (4k x 4k) |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア | 名称: SPIDER / カテゴリ: 3次元再構成 | ||||||||||||
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CTF補正 | 詳細: each subvolume | ||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||
3次元再構成 | 手法: Projection matching / 解像度: 6 Å / 解像度の算出法: FSC 0.5 CUT-OFF / 粒子像の数: 134500 / ピクセルサイズ(公称値): 1.2375 Å / ピクセルサイズ(実測値): 1.2375 Å / 対称性のタイプ: POINT | ||||||||||||
精密化ステップ | サイクル: LAST
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