+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-40707 | |||||||||
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タイトル | SARS-CoV-2 replication-transcription complex bound to RNA-nsp9, as a noncatalytic RNA-nsp9 binding mode | |||||||||
マップデータ | Composite sharpened map | |||||||||
試料 |
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キーワード | RTC / nsp12 / nsp9 / NiRAN / SARS-CoV-2 / deRNAylation / mRNA capping / UMPCPP / VIRAL PROTEIN | |||||||||
機能・相同性 | 機能・相同性情報 protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / 付加脱離酵素(リアーゼ); P-Oリアーゼ類; - / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs ...protein guanylyltransferase activity / RNA endonuclease activity, producing 3'-phosphomonoesters / mRNA guanylyltransferase activity / 5'-3' RNA helicase activity / 付加脱離酵素(リアーゼ); P-Oリアーゼ類; - / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / Assembly of the SARS-CoV-2 Replication-Transcription Complex (RTC) / Maturation of replicase proteins / ISG15-specific peptidase activity / Transcription of SARS-CoV-2 sgRNAs / Translation of Replicase and Assembly of the Replication Transcription Complex / TRAF3-dependent IRF activation pathway / Replication of the SARS-CoV-2 genome / snRNP Assembly / double membrane vesicle viral factory outer membrane / 加水分解酵素; エステル加水分解酵素; 5'-リン酸モノエステル産生エキソリボヌクレアーゼ / 5'-3' DNA helicase activity / SARS coronavirus main proteinase / 3'-5'-RNA exonuclease activity / host cell endoplasmic reticulum-Golgi intermediate compartment / host cell endosome / symbiont-mediated suppression of host toll-like receptor signaling pathway / symbiont-mediated degradation of host mRNA / mRNA guanylyltransferase / symbiont-mediated suppression of host ISG15-protein conjugation / G-quadruplex RNA binding / omega peptidase activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / SARS-CoV-2 modulates host translation machinery / mRNA (guanine-N7)-methyltransferase / host cell Golgi apparatus / methyltransferase cap1 / symbiont-mediated perturbation of host ubiquitin-like protein modification / DNA helicase / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; システインプロテアーゼ / single-stranded RNA binding / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / viral protein processing / lyase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / copper ion binding / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / lipid binding / host cell nucleus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane 類似検索 - 分子機能 | |||||||||
生物種 | Severe acute respiratory syndrome coronavirus 2 (ウイルス) / Severe acute respiratory syndrome coronavirus (SARS コロナウイルス) | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.06 Å | |||||||||
データ登録者 | Small GI / Darst SA / Campbell EA | |||||||||
資金援助 | 米国, 1件
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引用 | ジャーナル: Mol Cell / 年: 2023 タイトル: Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain. 著者: Gabriel I Small / Olga Fedorova / Paul Dominic B Olinares / Joshua Chandanani / Anoosha Banerjee / Young Joo Choi / Henrik Molina / Brian T Chait / Seth A Darst / Elizabeth A Campbell / 要旨: The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with ...The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5' cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here, we determine high-resolution cryoelectron microscopy (cryo-EM) structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development. | |||||||||
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_40707.map.gz | 58.4 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-40707-v30.xml emd-40707.xml | 28.4 KB 28.4 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_40707_fsc.xml | 8.4 KB | 表示 | FSCデータファイル |
画像 | emd_40707.png | 44 KB | ||
Filedesc metadata | emd-40707.cif.gz | 7.2 KB | ||
その他 | emd_40707_additional_1.map.gz emd_40707_additional_2.map.gz emd_40707_additional_3.map.gz emd_40707_half_map_1.map.gz emd_40707_half_map_2.map.gz | 14 MB 59.7 MB 59.6 MB 59.4 MB 59.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-40707 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-40707 | 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_40707.map.gz / 形式: CCP4 / 大きさ: 64 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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注釈 | Composite sharpened map | ||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 1.0825 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
-追加マップ: Composite locally filtered map
ファイル | emd_40707_additional_1.map | ||||||||||||
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注釈 | Composite 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: Consensus map used in composite
ファイル | emd_40707_additional_2.map | ||||||||||||
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注釈 | Consensus map used in composite | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-追加マップ: Focused refinement map used in composite
ファイル | emd_40707_additional_3.map | ||||||||||||
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注釈 | Focused refinement map used in composite | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Composite half map A
ファイル | emd_40707_half_map_1.map | ||||||||||||
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注釈 | Composite half map A | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: Composite half map B
ファイル | emd_40707_half_map_2.map | ||||||||||||
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注釈 | Composite half map B | ||||||||||||
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 : SARS-CoV-2 replication-transcription complex bound to RNA-nsp9, a...
+超分子 #1: SARS-CoV-2 replication-transcription complex bound to RNA-nsp9, a...
+分子 #1: RNA-directed RNA polymerase
+分子 #2: Non-structural protein 8
+分子 #3: Non-structural protein 7
+分子 #4: Non-structural protein 9
+分子 #5: Primer RNA
+分子 #6: Template RNA
+分子 #7: SARS-CoV-2 5' UTR
+分子 #8: 5'-O-[(R)-hydroxy(thiophosphonooxy)phosphoryl]guanosine
+分子 #9: MAGNESIUM ION
+分子 #10: ZINC ION
+分子 #11: 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: 8 |
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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: 51.51 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): 1.8 µm / 最小 デフォーカス(公称値): 0.8 µm |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |