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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) | |||||||||
![]() | Unsharpened Refine3D map | |||||||||
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![]() | Human 80S / tRNA / mRNA eEF1A / eIF5A / tRNA selection / RIBOSOME | |||||||||
機能・相同性 | ![]() cytoplasmic side of lysosomal membrane / regulation of D-erythro-sphingosine kinase activity / Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / regulation of chaperone-mediated autophagy / positive regulation by host of viral genome replication / 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 / eukaryotic 80S initiation complex ...cytoplasmic side of lysosomal membrane / regulation of D-erythro-sphingosine kinase activity / Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / regulation of chaperone-mediated autophagy / positive regulation by host of viral genome replication / 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 / eukaryotic 80S initiation complex / response to TNF agonist / positive regulation of base-excision repair / negative regulation of protein neddylation / protein tyrosine kinase inhibitor activity / embryonic brain development / positive regulation of respiratory burst involved in inflammatory response / translation at presynapse / 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 / axial mesoderm development / nucleolus organization / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / IRE1-RACK1-PP2A complex / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / 90S preribosome assembly / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / TORC2 complex binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / GAIT complex / neural crest cell differentiation / NF-kappaB complex / middle ear morphogenesis / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / positive regulation of ubiquitin-protein transferase activity / 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 / A band / laminin receptor activity / alpha-beta T cell differentiation / regulation of G1 to G0 transition / exit from mitosis / protein kinase A binding / 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 / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / optic nerve development / Translation initiation complex formation / pigmentation / positive regulation of mitochondrial depolarization / response to aldosterone / mammalian oogenesis stage / cortical actin cytoskeleton / retinal ganglion cell axon guidance / G1 to G0 transition / homeostatic process / activation-induced cell death of T cells / positive regulation of T cell receptor signaling pathway / negative regulation of Wnt signaling pathway / lung morphogenesis / fibroblast growth factor binding / 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 / macrophage chemotaxis / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / monocyte chemotaxis / Selenocysteine synthesis / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / phagocytic cup / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / translational elongation / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction 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: 2.8 Å | |||||||||
![]() | Holm M / Natchiar KS / Rundlet EJ / Myasnikov AG / Altman RB / Blanchard SC | |||||||||
資金援助 | 1件
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![]() | ![]() 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. | |||||||||
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構造の表示
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ダウンロードとリンク
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マップデータ | ![]() | 2.2 GB | ![]() | |
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ヘッダ (付随情報) | ![]() ![]() | 117.3 KB 117.3 KB | 表示 表示 | ![]() |
FSC (解像度算出) | ![]() | 31.7 KB | 表示 | ![]() |
画像 | ![]() | 182.2 KB | ||
マスクデータ | ![]() | 2.7 GB | ![]() | |
Filedesc metadata | ![]() | 22.7 KB | ||
その他 | ![]() ![]() ![]() ![]() ![]() | 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 | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 1.2 MB | 表示 | ![]() |
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文書・詳細版 | ![]() | 1.2 MB | 表示 | |
XML形式データ | ![]() | 40 KB | 表示 | |
CIF形式データ | ![]() | 53.8 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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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
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注釈 | Unsharpened Refine3D map | ||||||||||||||||||||
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
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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 | ||||||||||||
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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 | ||||||||||||
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 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 | ||||||||||||
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 : 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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![]() | 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: ![]() |
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: |