+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-16052 | ||||||||||||||||||
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タイトル | Cryo-EM structure of stalled rabbit 80S ribosomes in complex with human CCR4-NOT and CNOT4 | ||||||||||||||||||
マップデータ | Postprocessed map | ||||||||||||||||||
試料 |
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キーワード | translational control / mRNA decay / deadenylation / ribosome stalling / human CCR4-NOT / RIBOSOME | ||||||||||||||||||
機能・相同性 | 機能・相同性情報 CCR4-NOT core complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / regulatory ncRNA-mediated gene silencing / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator ...CCR4-NOT core complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / regulatory ncRNA-mediated gene silencing / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / TOR signaling / T cell proliferation involved in immune response / protein-RNA complex assembly / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / cytosolic ribosome / rough endoplasmic reticulum / 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 / rescue of stalled ribosome / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / ribosomal large subunit biogenesis / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / positive regulation of translation / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / P-body / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / modification-dependent protein catabolic process / cytoplasmic ribonucleoprotein granule / spindle / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosome biogenesis / ribosome binding / glucose homeostasis / 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 / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / cell cycle / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell division / DNA repair / mRNA binding / apoptotic process / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / regulation of DNA-templated transcription / nucleolus / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding 類似検索 - 分子機能 | ||||||||||||||||||
生物種 | Oryctolagus cuniculus (ウサギ) / 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: 3.1 Å | ||||||||||||||||||
データ登録者 | Absmeier E / Chandrasekaran V / O'Reilly FJ / Stowell JAW / Rappsilber J / Passmore LA | ||||||||||||||||||
資金援助 | 英国, ドイツ, 5件
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引用 | ジャーナル: Nat Struct Mol Biol / 年: 2023 タイトル: Modulation of GluA2-γ5 synaptic complex desensitization, polyamine block and antiepileptic perampanel inhibition by auxiliary subunit cornichon-2. 著者: Shanti Pal Gangwar / Laura Y Yen / Maria V Yelshanskaya / Aryeh Korman / Drew R Jones / Alexander I Sobolevsky / 要旨: Synaptic complexes of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors (AMPARs) with auxiliary subunits mediate most excitatory neurotransmission and can be targeted to treat ...Synaptic complexes of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors (AMPARs) with auxiliary subunits mediate most excitatory neurotransmission and can be targeted to treat neuropsychiatric and neurological disorders, including epilepsy. Here we present cryogenic-electron microscopy structures of rat GluA2 AMPAR complexes with inhibitory mouse γ5 and potentiating human cornichon-2 (CNIH2) auxiliary subunits. CNIH2 appears to destabilize the desensitized state of the complex by reducing the separation of the upper lobes in ligand-binding domain dimers. At the same time, CNIH2 stabilizes binding of polyamine spermidine to the selectivity filter of the closed ion channel. Nevertheless, CNIH2, and to a lesser extent γ5, attenuate polyamine block of the open channel and reduce the potency of the antiepileptic drug perampanel that inhibits the synaptic complex allosterically by binding to sites in the ion channel extracellular collar. These findings illustrate the fine-tuning of synaptic complex structure and function in an auxiliary subunit-dependent manner, which is critical for the study of brain region-specific neurotransmission and design of therapeutics for disease treatment. | ||||||||||||||||||
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_16052.map.gz | 99.1 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-16052-v30.xml emd-16052.xml | 108 KB 108 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_16052_fsc.xml | 17.7 KB | 表示 | FSCデータファイル |
画像 | emd_16052.png | 202.6 KB | ||
マスクデータ | emd_16052_msk_1.map | 476.8 MB | マスクマップ | |
Filedesc metadata | emd-16052.cif.gz | 20.2 KB | ||
その他 | emd_16052_additional_1.map.gz emd_16052_additional_2.map.gz emd_16052_half_map_1.map.gz emd_16052_half_map_2.map.gz | 15.5 MB 382 MB 383.3 MB 383.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-16052 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16052 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_16052_validation.pdf.gz | 1.1 MB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_16052_full_validation.pdf.gz | 1.1 MB | 表示 | |
XML形式データ | emd_16052_validation.xml.gz | 25.5 KB | 表示 | |
CIF形式データ | emd_16052_validation.cif.gz | 34 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16052 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16052 | HTTPS FTP |
-関連構造データ
関連構造データ | 8bhfMC 8ss2C 8ss3C 8ss4C 8ss5C 8ss6C 8ss7C 8ss8C 8ss9C 8ssaC 8ssbC M: このマップから作成された原子モデル C: 同じ文献を引用 (文献) |
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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 |
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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_16052.map.gz / 形式: CCP4 / 大きさ: 476.8 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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注釈 | Postprocessed 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: 0.829 Å | ||||||||||||||||||||||||||||||||||||
密度 |
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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_16052_msk_1.map | ||||||||||||
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投影像・断面図 |
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密度ヒストグラム |
-追加マップ: 2-fold downscaled map used for interpretation
ファイル | emd_16052_additional_1.map | ||||||||||||
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注釈 | 2-fold downscaled map used for interpretation | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Refined map before postprocessing
ファイル | emd_16052_additional_2.map | ||||||||||||
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注釈 | Refined map before postprocessing | ||||||||||||
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 1 map
ファイル | emd_16052_half_map_1.map | ||||||||||||
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注釈 | Half 1 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 2 map
ファイル | emd_16052_half_map_2.map | ||||||||||||
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注釈 | Half 2 map | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-試料の構成要素
+全体 : Ribosome complex
+超分子 #1: Ribosome complex
+分子 #1: Ribosomal protein L15
+分子 #2: 60S ribosomal protein L13a
+分子 #3: 60S ribosomal protein L17
+分子 #4: Ribosomal protein L18
+分子 #5: Ribosomal protein L19
+分子 #6: 60S ribosomal protein L18a
+分子 #7: 60S ribosomal protein L21
+分子 #8: 60S ribosomal protein L22
+分子 #9: 60S ribosomal protein L23
+分子 #10: TRASH domain-containing protein
+分子 #11: Ribosomal protein L23/L25 N-terminal domain-containing protein
+分子 #12: Ribosomal protein L26
+分子 #13: 60S ribosomal protein L27
+分子 #14: 60S ribosomal protein L27a
+分子 #15: 60S ribosomal protein L29
+分子 #16: 60S ribosomal protein L30
+分子 #17: 60S ribosomal protein L31
+分子 #18: Ribosomal protein L32
+分子 #19: 60S ribosomal protein L35a
+分子 #20: 60S ribosomal protein L34
+分子 #21: 60S ribosomal protein L35
+分子 #22: 60S ribosomal protein L36
+分子 #23: Ribosomal protein L37
+分子 #24: 60S ribosomal protein L38
+分子 #25: 60S ribosomal protein L39-like
+分子 #26: Ubiquitin-60S ribosomal protein L40
+分子 #27: 60S ribosomal protein L41
+分子 #28: Ribosomal protein L36a like
+分子 #29: 60S ribosomal protein L37a
+分子 #30: 60S ribosomal protein L28
+分子 #31: 60S acidic ribosomal protein P0
+分子 #32: 60S ribosomal protein L12
+分子 #33: 60S ribosomal protein L10a
+分子 #35: CCR4-NOT transcription complex subunit 3
+分子 #37: nascent chain
+分子 #42: 40S_SA_C domain-containing protein
+分子 #43: 40S ribosomal protein S3a
+分子 #44: 40S ribosomal protein S2
+分子 #45: Ribosomal protein S3
+分子 #46: 40S ribosomal protein S4
+分子 #47: Ribosomal protein S5
+分子 #48: 40S ribosomal protein S6
+分子 #49: 40S ribosomal protein S7
+分子 #50: 40S ribosomal protein S8
+分子 #51: Ribosomal protein S9 (Predicted)
+分子 #52: Plectin/S10 N-terminal domain-containing protein
+分子 #53: 40S ribosomal protein S11
+分子 #54: 40S ribosomal protein S12
+分子 #55: ribosomal protein uS15
+分子 #56: Ribosomal protein S14
+分子 #57: 40S ribosomal protein S15
+分子 #58: Ribosomal protein S16
+分子 #59: 40S ribosomal protein S17
+分子 #60: 40S ribosomal protein S18
+分子 #61: 40S ribosomal protein S19
+分子 #62: Ribosomal protein S20
+分子 #63: 40S ribosomal protein S21
+分子 #64: Ribosomal protein S15a
+分子 #65: Ribosomal protein S23
+分子 #66: 40S ribosomal protein S24
+分子 #67: 40S ribosomal protein S25
+分子 #68: 40S ribosomal protein S26
+分子 #69: 40S ribosomal protein S27
+分子 #70: Ribosomal protein S28
+分子 #71: 40S ribosomal protein S29
+分子 #72: Ubiquitin-like domain-containing protein
+分子 #73: Ubiquitin-40S ribosomal protein S27a
+分子 #74: Ribosomal protein RACK1
+分子 #75: 60S ribosomal protein L8
+分子 #76: Ribosomal protein L3
+分子 #77: 60S ribosomal protein L4
+分子 #78: 60S ribosomal protein L5
+分子 #79: 60S ribosomal protein L6
+分子 #80: 60S ribosomal protein L7
+分子 #81: 60S ribosomal protein L7a
+分子 #82: 60S ribosomal protein L9
+分子 #83: Ribosomal protein L10
+分子 #84: 60S ribosomal protein L11
+分子 #85: 60S ribosomal protein L13
+分子 #86: 60S ribosomal protein L14
+分子 #34: mRNA
+分子 #36: P-site tRNA
+分子 #38: 28S ribosomal RNA
+分子 #39: 5S ribosomal RNA
+分子 #40: 5.8S ribosomal RNA
+分子 #41: 18S ribosomal RNA
+分子 #87: MAGNESIUM ION
+分子 #88: ZINC ION
-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 |
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凍結 | 凍結剤: ETHANE |
-電子顕微鏡法
顕微鏡 | TFS KRIOS |
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撮影 | フィルム・検出器のモデル: GATAN K3 BIOQUANTUM (6k x 4k) 平均電子線量: 47.5 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): 3.0 µm / 最小 デフォーカス(公称値): 0.9 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |