+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-4242 | |||||||||
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タイトル | Human cap-dependent 48S pre-initiation complex | |||||||||
マップデータ | human 48S pre-initiation complex, reconstituted in the presence of capped mRNA, eIF4B and eIF4F, displaying eIF2 ternary complex, eIF3 and eIF4B | |||||||||
試料 |
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機能・相同性 | 機能・相同性情報 positive regulation of mRNA binding / Cellular response to mitochondrial stress / viral translational termination-reinitiation / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3e / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Response of EIF2AK1 (HRI) to heme deficiency / eukaryotic translation initiation factor 3 complex, eIF3m / Recycling of eIF2:GDP / PERK regulates gene expression ...positive regulation of mRNA binding / Cellular response to mitochondrial stress / viral translational termination-reinitiation / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3e / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Response of EIF2AK1 (HRI) to heme deficiency / eukaryotic translation initiation factor 3 complex, eIF3m / Recycling of eIF2:GDP / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / formation of cytoplasmic translation initiation complex / eukaryotic translation initiation factor 3 complex / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / protein-synthesizing GTPase / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / translation factor activity, RNA binding / formation of translation preinitiation complex / Deadenylation of mRNA / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / eukaryotic 48S preinitiation complex / protein tyrosine kinase inhibitor activity / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / M-decay: degradation of maternal mRNAs by maternally stored factors / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / regulation of translational initiation / regulation of establishment of cell polarity / negative regulation of phagocytosis / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / protein kinase A binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / Translation initiation complex formation / pigmentation / positive regulation of mitochondrial depolarization / mammalian oogenesis stage / activation-induced cell death of T cells / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / regulation of cell division / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / phagocytic cup / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / cyclin binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / TOR signaling / L13a-mediated translational silencing of Ceruloplasmin expression / positive regulation of DNA repair / T cell proliferation involved in immune response / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / translation regulator activity 類似検索 - 分子機能 | |||||||||
生物種 | Homo sapiens (ヒト) / Human (ヒト) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 6.3 Å | |||||||||
データ登録者 | Schaffitzel C | |||||||||
引用 | ジャーナル: Nucleic Acids Res / 年: 2018 タイトル: Structure of a human cap-dependent 48S translation pre-initiation complex. 著者: Boris Eliseev / Lahari Yeramala / Alexander Leitner / Manikandan Karuppasamy / Etienne Raimondeau / Karine Huard / Elena Alkalaeva / Ruedi Aebersold / Christiane Schaffitzel / 要旨: Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load ...Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load the mRNA onto the 43S pre-initiation complex comprising 40S and initiation factors 1, 1A, 2, 3 and 5 as well as initiator-tRNA. Binding of the mRNA is followed by mRNA scanning in the 48S pre-initiation complex, until a start codon is recognised. Here, we use a reconstituted system to prepare human 48S complexes assembled on capped mRNA in the presence of eIF4B and eIF4F. The highly purified h-48S complexes are used for cross-linking/mass spectrometry, revealing the protein interaction network in this complex. We report the electron cryo-microscopy structure of the h-48S complex at 6.3 Å resolution. While the majority of eIF4B and eIF4F appear to be flexible with respect to the ribosome, additional density is detected at the entrance of the 40S mRNA channel which we attribute to the RNA-recognition motif of eIF4B. The eight core subunits of eIF3 are bound at the 40S solvent-exposed side, as well as the subunits eIF3d, eIF3b and eIF3i. elF2 and initiator-tRNA bound to the start codon are present at the 40S intersubunit side. This cryo-EM structure represents a molecular snap-shot revealing the h-48S complex following start codon recognition. | |||||||||
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 | EMマップ: SurfViewMolmilJmol/JSmol |
添付画像 |
-ダウンロードとリンク
-EMDBアーカイブ
マップデータ | emd_4242.map.gz | 32.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-4242-v30.xml emd-4242.xml | 71.1 KB 71.1 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_4242.png | 56.4 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-4242 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4242 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_4242_validation.pdf.gz | 337.5 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_4242_full_validation.pdf.gz | 336.7 KB | 表示 | |
XML形式データ | emd_4242_validation.xml.gz | 5.1 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4242 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4242 | HTTPS FTP |
-関連構造データ
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
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「今月の分子」の関連する項目 |
-マップ
ファイル | ダウンロード / ファイル: emd_4242.map.gz / 形式: CCP4 / 大きさ: 34.3 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | human 48S pre-initiation complex, reconstituted in the presence of capped mRNA, eIF4B and eIF4F, displaying eIF2 ternary complex, eIF3 and eIF4B | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 2.5 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-試料の構成要素
+全体 : human cap-dependent 48S translation pre-initiation complex
+超分子 #1: human cap-dependent 48S translation pre-initiation complex
+超分子 #2: human cap-dependent 48S translation pre-initiation complex
+超分子 #3: mRNA
+超分子 #4: Eukaryotic translation initiation factor 4B
+分子 #1: Eukaryotic translation initiation factor 3 subunit A
+分子 #2: Eukaryotic translation initiation factor 3 subunit C
+分子 #3: Eukaryotic translation initiation factor 3 subunit E
+分子 #4: Eukaryotic translation initiation factor 3 subunit F
+分子 #5: Eukaryotic translation initiation factor 3 subunit H
+分子 #6: Eukaryotic translation initiation factor 3 subunit K
+分子 #7: Eukaryotic translation initiation factor 3 subunit L
+分子 #8: Eukaryotic translation initiation factor 3 subunit M
+分子 #9: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT D
+分子 #12: 40S ribosomal protein S11
+分子 #13: 40S ribosomal protein S16
+分子 #14: 40S ribosomal protein S4, X isoform
+分子 #15: 40S ribosomal protein S29
+分子 #16: 40S ribosomal protein S9
+分子 #17: 40S ribosomal protein S18
+分子 #19: Eukaryotic translation initiation factor 2 subunit 1
+分子 #20: 40S ribosomal protein S23
+分子 #21: 40S ribosomal protein S19
+分子 #22: Eukaryotic translation initiation factor 2 subunit 3
+分子 #23: 40S ribosomal protein S5
+分子 #24: 40S ribosomal protein S30
+分子 #25: 40S ribosomal protein S25
+分子 #26: 40S ribosomal protein S7
+分子 #27: 40S ribosomal protein S27
+分子 #28: 40S ribosomal protein S13
+分子 #29: 40S ribosomal protein S15a
+分子 #30: 40S ribosomal protein S21
+分子 #31: 40S ribosomal protein S2
+分子 #32: EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT (eIF2-Beta)
+分子 #33: 40S ribosomal protein S17
+分子 #34: 40S ribosomal protein SA
+分子 #35: 40S ribosomal protein S3
+分子 #36: 40S ribosomal protein S20
+分子 #37: 40S ribosomal protein S3a
+分子 #38: 40S ribosomal protein S14
+分子 #39: 40S ribosomal protein S26
+分子 #40: 40S ribosomal protein S28
+分子 #41: Receptor of activated protein C kinase 1
+分子 #42: 40S ribosomal protein S15
+分子 #43: 40S ribosomal protein S8
+分子 #44: Ubiquitin-40S ribosomal protein S27a
+分子 #45: 40S ribosomal protein S6
+分子 #46: 40S ribosomal protein S12
+分子 #47: 40S ribosomal protein S24
+分子 #48: 40S ribosomal protein S10
+分子 #49: Eukaryotic translation initiation factor 4B
+分子 #50: Eukaryotic translation initiation factor 3 subunit B
+分子 #10: 18S ribosomal RNA
+分子 #11: Messenger RNA (26-MER)
+分子 #18: Transfer RNA (75-MER)
+分子 #51: 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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解析 | 単粒子再構成法 |
試料の集合状態 | particle |
-試料調製
緩衝液 | pH: 7.5 詳細: 20 mM Tris HCl, 50 mM KOAc, 2.5 mM MgCl2, 2 mM DTT, 0.25 mM spermidine 0.25 mM GMPPNP |
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グリッド | モデル: Quantifoil R2/2 |
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277 K / 装置: FEI VITROBOT MARK IV |
-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: FEI FALCON II (4k x 4k) 検出モード: INTEGRATING / 平均電子線量: 30.0 e/Å2 |
電子線 | 加速電圧: 300 kV / 電子線源: FIELD EMISSION GUN |
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): 4.0 µm / 最小 デフォーカス(公称値): 1.5 µm / 倍率(公称値): 112000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
+画像解析
-原子モデル構築 1
精密化 | 空間: REAL / プロトコル: RIGID BODY FIT 当てはまり具合の基準: Cross-correlation coefficient |
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得られたモデル | PDB-6fec: |