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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 | mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2) | |||||||||
マップデータ | Unsharpened Refine3D map | |||||||||
試料 |
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キーワード | Human 80S / tRNA / mRNA eEF1A / eIF5A / tRNA selection / RIBOSOME | |||||||||
| 機能・相同性 | 機能・相同性情報cytoplasmic side of lysosomal membrane / Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / regulation of chaperone-mediated autophagy / host-mediated activation of viral genome replication / embryonic brain development / translation at presynapse / exit from mitosis / optic nerve development / regulation of translation involved in cellular response to UV ...cytoplasmic side of lysosomal membrane / Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / regulation of chaperone-mediated autophagy / host-mediated activation of viral genome replication / embryonic brain development / translation at presynapse / exit from mitosis / optic nerve development / regulation of translation involved in cellular response to UV / eukaryotic 80S initiation complex / negative regulation of formation of translation preinitiation complex / axial mesoderm development / negative regulation of endoplasmic reticulum unfolded protein response / ribosomal protein import into nucleus / regulation of G1 to G0 transition / retinal ganglion cell axon guidance / kinase activator activity / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of ubiquitin-protein transferase activity / protein-DNA complex disassembly / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of gastrulation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / nucleolus organization / positive regulation of DNA-templated transcription initiation / alpha-beta T cell differentiation / TNFR1-mediated ceramide production / positive regulation of DNA damage response, signal transduction by p53 class mediator / GAIT complex / negative regulation of RNA splicing / TORC2 complex binding / neural crest cell differentiation / supercoiled DNA binding / NF-kappaB complex / negative regulation of DNA repair / G1 to G0 transition / cytoplasmic translational initiation / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / middle ear morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / rRNA modification in the nucleus and cytosol / cortical actin cytoskeleton / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / ion channel inhibitor activity / laminin receptor activity / protein kinase A binding / homeostatic process / pigmentation / Ribosomal scanning and start codon recognition / positive regulation of mitochondrial depolarization / Translation initiation complex formation / macrophage chemotaxis / lung morphogenesis / negative regulation of Wnt signaling pathway / positive regulation of natural killer cell proliferation / fibroblast growth factor binding / monocyte chemotaxis / BH3 domain binding / Protein hydroxylation / negative regulation of translational frameshifting / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / TOR signaling / positive regulation of GTPase activity / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / iron-sulfur cluster binding / regulation of cell division / Peptide chain elongation / translational elongation / cellular response to ethanol / Selenocysteine synthesis / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Formation of a pool of free 40S subunits / negative regulation of protein binding / protein serine/threonine kinase inhibitor activity / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of respiratory burst involved in inflammatory response / HSF1 activation / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Viral mRNA Translation / positive regulation of signal transduction by p53 class mediator / protein localization to nucleus 類似検索 - 分子機能 | |||||||||
| 生物種 | Homo sapiens (ヒト) | |||||||||
| 手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 2.8 Å | |||||||||
データ登録者 | Holm M / Natchiar KS / Rundlet EJ / Myasnikov AG / Altman RB / Blanchard SC | |||||||||
| 資金援助 | 1件
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引用 | ジャーナル: Nature / 年: 2023タイトル: mRNA decoding in human is kinetically and structurally distinct from bacteria. 著者: Mikael Holm / S Kundhavai Natchiar / Emily J Rundlet / Alexander G Myasnikov / Zoe L Watson / Roger B Altman / Hao-Yuan Wang / Jack Taunton / Scott C Blanchard / ![]() 要旨: In all species, ribosomes synthesize proteins by faithfully decoding messenger RNA (mRNA) nucleotide sequences using aminoacyl-tRNA substrates. Current knowledge of the decoding mechanism derives ...In all species, ribosomes synthesize proteins by faithfully decoding messenger RNA (mRNA) nucleotide sequences using aminoacyl-tRNA substrates. Current knowledge of the decoding mechanism derives principally from studies on bacterial systems. Although key features are conserved across evolution, eukaryotes achieve higher-fidelity mRNA decoding than bacteria. In human, changes in decoding fidelity are linked to ageing and disease and represent a potential point of therapeutic intervention in both viral and cancer treatment. Here we combine single-molecule imaging and cryogenic electron microscopy methods to examine the molecular basis of human ribosome fidelity to reveal that the decoding mechanism is both kinetically and structurally distinct from that of bacteria. Although decoding is globally analogous in both species, the reaction coordinate of aminoacyl-tRNA movement is altered on the human ribosome and the process is an order of magnitude slower. These distinctions arise from eukaryote-specific structural elements in the human ribosome and in the elongation factor eukaryotic elongation factor 1A (eEF1A) that together coordinate faithful tRNA incorporation at each mRNA codon. The distinct nature and timing of conformational changes within the ribosome and eEF1A rationalize how increased decoding fidelity is achieved and potentially regulated in eukaryotic species. | |||||||||
| 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 | emd_29771.map.gz | 2.2 GB | EMDBマップデータ形式 | |
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| ヘッダ (付随情報) | emd-29771-v30.xml emd-29771.xml | 117.3 KB 117.3 KB | 表示 表示 | EMDBヘッダ |
| FSC (解像度算出) | emd_29771_fsc.xml | 31.7 KB | 表示 | FSCデータファイル |
| 画像 | emd_29771.png | 182.2 KB | ||
| マスクデータ | emd_29771_msk_1.map | 2.7 GB | マスクマップ | |
| Filedesc metadata | emd-29771.cif.gz | 22.7 KB | ||
| その他 | emd_29771_additional_1.map.gz emd_29771_additional_2.map.gz emd_29771_additional_3.map.gz emd_29771_half_map_1.map.gz emd_29771_half_map_2.map.gz | 1.5 GB 2.5 GB 185.8 MB 2.2 GB 2.2 GB | ||
| アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-29771 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29771 | HTTPS FTP |
-関連構造データ
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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 |
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マップ
| ファイル | ダウンロード / ファイル: emd_29771.map.gz / 形式: CCP4 / 大きさ: 2.7 GB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| 注釈 | Unsharpened Refine3D map | ||||||||||||||||||||||||||||||||||||
| 投影像・断面図 | 画像のコントロール
画像は Spider により作成 | ||||||||||||||||||||||||||||||||||||
| ボクセルのサイズ | X=Y=Z: 0.6472 Å | ||||||||||||||||||||||||||||||||||||
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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 | emd_29771_msk_1.map | ||||||||||||
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| 密度ヒストグラム |
-追加マップ: Post-processed locally filtered map
| ファイル | emd_29771_additional_1.map | ||||||||||||
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| 注釈 | Post-processed locally filtered map | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
-追加マップ: Post-processed map
| ファイル | emd_29771_additional_2.map | ||||||||||||
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| 注釈 | Post-processed map | ||||||||||||
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| 密度ヒストグラム |
-追加マップ: Post-processed masked map
| ファイル | emd_29771_additional_3.map | ||||||||||||
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| 注釈 | Post-processed masked map | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
-ハーフマップ: Half map 1
| ファイル | emd_29771_half_map_1.map | ||||||||||||
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| 注釈 | Half map 1 | ||||||||||||
| 投影像・断面図 |
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| 密度ヒストグラム |
-ハーフマップ: Half map 2
| ファイル | emd_29771_half_map_2.map | ||||||||||||
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| 注釈 | Half map 2 | ||||||||||||
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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 : Human ribosome
+超分子 #1: Human ribosome
+分子 #1: 18S rRNA
+分子 #2: 5.8S rRNA
+分子 #3: 28S rRNA
+分子 #4: 5S rRNA
+分子 #83: mRNA
+分子 #84: A-site tRNA
+分子 #85: P-site tRNA
+分子 #5: 40S ribosomal protein S3a
+分子 #6: 40S ribosomal protein SA
+分子 #7: 40S ribosomal protein S3
+分子 #8: 40S ribosomal protein S9
+分子 #9: 40S ribosomal protein S4, X isoform
+分子 #10: 40S ribosomal protein S2
+分子 #11: 40S ribosomal protein S6
+分子 #12: 40S ribosomal protein S5
+分子 #13: 40S ribosomal protein S7
+分子 #14: 40S ribosomal protein S15a
+分子 #15: 40S ribosomal protein S8
+分子 #16: 40S ribosomal protein S16
+分子 #17: 40S ribosomal protein S20
+分子 #18: 40S ribosomal protein S10
+分子 #19: 40S ribosomal protein S14
+分子 #20: uS12
+分子 #21: 40S ribosomal protein S12
+分子 #22: 40S ribosomal protein S18
+分子 #23: 40S ribosomal protein S29
+分子 #24: 40S ribosomal protein S13
+分子 #25: 40S ribosomal protein S11
+分子 #26: 40S ribosomal protein S17
+分子 #27: 40S ribosomal protein S15
+分子 #28: 40S ribosomal protein S19
+分子 #29: 40S ribosomal protein S21
+分子 #30: 40S ribosomal protein S24
+分子 #31: 40S ribosomal protein S25
+分子 #32: 40S ribosomal protein S26
+分子 #33: 40S ribosomal protein S27
+分子 #34: 40S ribosomal protein S28
+分子 #35: FAU ubiquitin-like and ribosomal protein S30
+分子 #36: Ubiquitin-40S ribosomal protein S27a
+分子 #37: Receptor of activated protein C kinase 1
+分子 #38: 60S ribosomal protein L10a
+分子 #39: uL2
+分子 #40: 60S ribosomal protein L3
+分子 #41: 60S ribosomal protein L4
+分子 #42: 60S ribosomal protein L11
+分子 #43: 60S ribosomal protein L9
+分子 #44: 60S ribosomal protein L6
+分子 #45: 60S ribosomal protein L7a
+分子 #46: 60S acidic ribosomal protein P0
+分子 #47: 60S ribosomal protein L12
+分子 #48: 60S ribosomal protein L13a
+分子 #49: eL13
+分子 #50: 60S ribosomal protein L23
+分子 #51: 60S ribosomal protein L14
+分子 #52: 60S ribosomal protein L27a
+分子 #53: 60S ribosomal protein L15
+分子 #54: 60S ribosomal protein L10
+分子 #55: 60S ribosomal protein L5
+分子 #56: 60S ribosomal protein L18
+分子 #57: 60S ribosomal protein L19
+分子 #58: 60S ribosomal protein L18a
+分子 #59: 60S ribosomal protein L21
+分子 #60: 60S ribosomal protein L17
+分子 #61: 60S ribosomal protein L22
+分子 #62: 60S ribosomal protein L23a
+分子 #63: 60S ribosomal protein L26
+分子 #64: 60S ribosomal protein L24
+分子 #65: 60S ribosomal protein L27
+分子 #66: 60S ribosomal protein L28
+分子 #67: 60S ribosomal protein L35
+分子 #68: 60S ribosomal protein L29
+分子 #69: 60S ribosomal protein L7
+分子 #70: 60S ribosomal protein L30
+分子 #71: 60S ribosomal protein L31
+分子 #72: 60S ribosomal protein L32
+分子 #73: 60S ribosomal protein L35a
+分子 #74: 60S ribosomal protein L34
+分子 #75: 60S ribosomal protein L36
+分子 #76: 60S ribosomal protein L37
+分子 #77: 60S ribosomal protein L38
+分子 #78: 60S ribosomal protein L39
+分子 #79: eL40
+分子 #80: 60S ribosomal protein L41
+分子 #81: 60S ribosomal protein L36a
+分子 #82: 60S ribosomal protein L37a
+分子 #86: Elongation factor 1-alpha 1
+分子 #87: SPERMIDINE
+分子 #88: POTASSIUM ION
+分子 #89: MAGNESIUM ION
+分子 #90: 1,4-DIAMINOBUTANE
+分子 #91: 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethy...
+分子 #92: (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methy...
+分子 #93: ZINC ION
+分子 #94: PHENYLALANINE
+分子 #95: METHIONINE
+分子 #96: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
+分子 #97: (3R,6R,9S,12S,15S,18S,20R,24aR)-6-[(2S)-butan-2-yl]-3,12-bis[(1R)...
+分子 #98: 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 |
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試料調製
| 濃度 | 4 mg/mL |
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| 緩衝液 | pH: 7 |
| 凍結 | 凍結剤: ETHANE / チャンバー内湿度: 95 % / チャンバー内温度: 283 K / 装置: FEI VITROBOT MARK IV |
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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 (6k x 4k) / 平均電子線量: 79.0 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): -1.5 µm / 最小 デフォーカス(公称値): -0.5 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 | プロトコル: OTHER |
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| 得られたモデル | ![]() PDB-8g6j: |
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コントローラー
万見について




キーワード
Homo sapiens (ヒト)
データ登録者
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FIELD EMISSION GUN

