+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-26444 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Mammalian 80S translation initiation complex with mRNA and Harringtonine | |||||||||
マップデータ | ||||||||||
試料 |
| |||||||||
機能・相同性 | 機能・相同性情報 ribosomal subunit / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / mammalian oogenesis stage / retinal ganglion cell axon guidance ...ribosomal subunit / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / mammalian oogenesis stage / retinal ganglion cell axon guidance / G1 to G0 transition / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cellular response to actinomycin D / cytosolic ribosome / rough endoplasmic reticulum / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / gastrulation / MDM2/MDM4 family protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / negative regulation of ubiquitin-dependent protein catabolic process / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / maturation of SSU-rRNA / positive regulation of translation / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / spindle / G1/S transition of mitotic cell cycle / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / rhythmic process / ribosome binding / glucose homeostasis / retina development in camera-type eye / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / 5S rRNA binding / large ribosomal subunit rRNA binding / perikaryon / cytosolic small ribosomal subunit / defense response to Gram-negative bacterium / killing of cells of another organism / cytosolic large ribosomal subunit / mitochondrial inner membrane / tRNA binding / cytoplasmic translation / postsynaptic density / cell differentiation / protein stabilization / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell cycle / cell division / DNA repair / mRNA binding / apoptotic process / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression / nucleolus / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / DNA binding / RNA binding 類似検索 - 分子機能 | |||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / rabbit (ウサギ) | |||||||||
手法 | 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 | Yang R / Arango D / Sturgill D / Oberdoerffer S | |||||||||
資金援助 | 米国, 1件
| |||||||||
引用 | ジャーナル: Mol Cell / 年: 2022 タイトル: Direct epitranscriptomic regulation of mammalian translation initiation through N4-acetylcytidine. 著者: Daniel Arango / David Sturgill / Renbin Yang / Tapan Kanai / Paulina Bauer / Jyoti Roy / Ziqiu Wang / Masaki Hosogane / Sarah Schiffers / Shalini Oberdoerffer / 要旨: mRNA function is influenced by modifications that modulate canonical nucleobase behavior. We show that a single modification mediates distinct impacts on mRNA translation in a position-dependent ...mRNA function is influenced by modifications that modulate canonical nucleobase behavior. We show that a single modification mediates distinct impacts on mRNA translation in a position-dependent manner. Although cytidine acetylation (ac4C) within protein-coding sequences stimulates translation, ac4C within 5' UTRs impacts protein synthesis at the level of initiation. 5' UTR acetylation promotes initiation at upstream sequences, competitively inhibiting annotated start codons. Acetylation further directly impedes initiation at optimal AUG contexts: ac4C within AUG-flanking Kozak sequences reduced initiation in base-resolved transcriptome-wide HeLa results and in vitro utilizing substrates with site-specific ac4C incorporation. Cryo-EM of mammalian 80S initiation complexes revealed that ac4C in the -1 position adjacent to an AUG start codon disrupts an interaction between C and hypermodified t6A at nucleotide 37 of the initiator tRNA. These findings demonstrate the impact of RNA modifications on nucleobase function at a molecular level and introduce mRNA acetylation as a factor regulating translation in a location-specific manner. | |||||||||
履歴 |
|
-構造の表示
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_26444.map.gz | 36.6 MB | EMDBマップデータ形式 | |
---|---|---|---|---|
ヘッダ (付随情報) | emd-26444-v30.xml emd-26444.xml | 85.3 KB 85.3 KB | 表示 表示 | EMDBヘッダ |
画像 | emd_26444.png | 71.9 KB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-26444 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26444 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_26444_validation.pdf.gz | 359.1 KB | 表示 | EMDB検証レポート |
---|---|---|---|---|
文書・詳細版 | emd_26444_full_validation.pdf.gz | 358.7 KB | 表示 | |
XML形式データ | emd_26444_validation.xml.gz | 7.6 KB | 表示 | |
CIF形式データ | emd_26444_validation.cif.gz | 8.8 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26444 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-26444 | HTTPS FTP |
-関連構造データ
関連構造データ | 7ucjMC 7uckC C: 同じ文献を引用 (文献) M: このマップから作成された原子モデル |
---|---|
類似構造データ | 類似検索 - 機能・相同性F&H 検索 |
-リンク
EMDBのページ | EMDB (EBI/PDBe) / EMDataResource |
---|---|
「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_26444.map.gz / 形式: CCP4 / 大きさ: 421.9 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ボクセルのサイズ | X=Y=Z: 1.358 Å | ||||||||||||||||||||
密度 |
| ||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||
詳細 | EMDB XML:
|
-添付データ
-試料の構成要素
+全体 : 80S translation initiation complex with C(-1) mRNA and Harringtonine
+超分子 #1: 80S translation initiation complex with C(-1) mRNA and Harringtonine
+分子 #1: P-site tRNA
+分子 #2: mRNA
+分子 #3: 28s rRNA
+分子 #4: 5S rRNA
+分子 #5: 5.8S rRNA
+分子 #6: 18S rRNA
+分子 #7: 60S ribosomal protein L8
+分子 #8: 60S ribosomal protein L3
+分子 #9: 60S ribosomal protein L4
+分子 #10: Ribosomal_L18_c domain-containing protein
+分子 #11: 60S ribosomal protein L6
+分子 #12: 60S ribosomal protein L7
+分子 #13: 60S ribosomal protein L7a
+分子 #14: 60S ribosomal protein L9
+分子 #15: Ribosomal protein L10
+分子 #16: 60S ribosomal protein L11
+分子 #17: 60S ribosomal protein L13
+分子 #18: 60S ribosomal protein L14
+分子 #19: 60S ribosomal protein L15
+分子 #20: 60S ribosomal protein L13a
+分子 #21: 60S ribosomal protein L17
+分子 #22: 60S ribosomal protein L18
+分子 #23: 60S ribosomal protein L19
+分子 #24: 60S ribosomal protein L18a
+分子 #25: 60S ribosomal protein L21
+分子 #26: 60S ribosomal protein L22
+分子 #27: 60S ribosomal protein L23
+分子 #28: Ribosomal protein L24
+分子 #29: 60S ribosomal protein L23a
+分子 #30: 60S ribosomal protein L26
+分子 #31: 60S ribosomal protein L27
+分子 #32: 60S ribosomal protein L27a
+分子 #33: 60S ribosomal protein L29
+分子 #34: 60S ribosomal protein L30
+分子 #35: 60S ribosomal protein L31
+分子 #36: 60S ribosomal protein L32
+分子 #37: 60S ribosomal protein L35a
+分子 #38: 60S ribosomal protein L34
+分子 #39: 60S ribosomal protein L35
+分子 #40: 60S ribosomal protein L36
+分子 #41: 60S ribosomal protein L37
+分子 #42: 60S ribosomal protein L38
+分子 #43: 60S ribosomal protein L39
+分子 #44: 60S ribosomal protein L40
+分子 #45: eL41
+分子 #46: 60S ribosomal protein L36a
+分子 #47: 60S ribosomal protein L37a
+分子 #48: 60S ribosomal protein L28
+分子 #49: 40S_SA_C domain-containing protein
+分子 #50: 40S ribosomal protein S3a
+分子 #51: 40S ribosomal protein S2
+分子 #52: 40S ribosomal protein S3
+分子 #53: 40S ribosomal protein S4
+分子 #54: Ribosomal protein S5
+分子 #55: 40S ribosomal protein S6
+分子 #56: 40S ribosomal protein S7
+分子 #57: 40S ribosomal protein S8
+分子 #58: 40S ribosomal protein S9
+分子 #59: 40S ribosomal protein S10
+分子 #60: 40S ribosomal protein S11
+分子 #61: 40S ribosomal protein S13
+分子 #62: 40S ribosomal protein S14
+分子 #63: 40S ribosomal protein S15
+分子 #64: 40S ribosomal protein S16
+分子 #65: 40S ribosomal protein S17
+分子 #66: 40S ribosomal protein S18
+分子 #67: 40S ribosomal protein S19
+分子 #68: 40S ribosomal protein S20
+分子 #69: eS21
+分子 #70: 40S ribosomal protein S15a
+分子 #71: 40S ribosomal protein S23
+分子 #72: 40S ribosomal protein S24
+分子 #73: 40S ribosomal protein S25
+分子 #74: eS26
+分子 #75: 40S ribosomal protein S27
+分子 #76: 40S ribosomal protein S28
+分子 #77: 40S ribosomal protein S29
+分子 #78: 40S ribosomal protein S30
+分子 #79: Receptor of activated protein C kinase 1
+分子 #80: MAGNESIUM ION
+分子 #81: Harringtonine
+分子 #82: ZINC ION
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
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 |
---|---|
凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
---|---|
撮影 | フィルム・検出器のモデル: GATAN K2 SUMMIT (4k x 4k) 平均電子線量: 50.0 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: OTHER / 撮影モード: BRIGHT FIELD / 最大 デフォーカス(公称値): 2.0 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 |
-画像解析
初期モデル | モデルのタイプ: OTHER / 詳細: By 3D volumes from negative staining dataset. |
---|---|
最終 再構成 | 解像度のタイプ: BY AUTHOR / 解像度: 3.1 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 使用した粒子像数: 52555 |
初期 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
最終 角度割当 | タイプ: MAXIMUM LIKELIHOOD |
-原子モデル構築 1
精密化 | 空間: REAL |
---|---|
得られたモデル | PDB-7ucj: |