+データを開く
-基本情報
登録情報 | データベース: EMDB / ID: EMD-23970 | |||||||||||||||
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タイトル | Full length SARS-CoV-2 Nsp2 | |||||||||||||||
マップデータ | SARS-CoV-2 Nsp2 main map | |||||||||||||||
試料 |
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キーワード | Nsp2 / virus infection / SARS-CoV-2 / Orf1a / 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 / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / 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) | |||||||||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.76 Å | |||||||||||||||
データ登録者 | QCRG Structural Biology Consortium | |||||||||||||||
資金援助 | 米国, 4件
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引用 | ジャーナル: bioRxiv / 年: 2021 タイトル: CryoEM and AI reveal a structure of SARS-CoV-2 Nsp2, a multifunctional protein involved in key host processes. 著者: Meghna Gupta / Caleigh M Azumaya / Michelle Moritz / Sergei Pourmal / Amy Diallo / Gregory E Merz / Gwendolyn Jang / Mehdi Bouhaddou / Andrea Fossati / Axel F Brilot / Devan Diwanji / Evelyn ...著者: Meghna Gupta / Caleigh M Azumaya / Michelle Moritz / Sergei Pourmal / Amy Diallo / Gregory E Merz / Gwendolyn Jang / Mehdi Bouhaddou / Andrea Fossati / Axel F Brilot / Devan Diwanji / Evelyn Hernandez / Nadia Herrera / Huong T Kratochvil / Victor L Lam / Fei Li / Yang Li / Henry C Nguyen / Carlos Nowotny / Tristan W Owens / Jessica K Peters / Alexandrea N Rizo / Ursula Schulze-Gahmen / Amber M Smith / Iris D Young / Zanlin Yu / Daniel Asarnow / Christian Billesbølle / Melody G Campbell / Jen Chen / Kuei-Ho Chen / Un Seng Chio / Miles Sasha Dickinson / Loan Doan / Mingliang Jin / Kate Kim / Junrui Li / Yen-Li Li / Edmond Linossi / Yanxin Liu / Megan Lo / Jocelyne Lopez / Kyle E Lopez / Adamo Mancino / Frank R Moss / Michael D Paul / Komal Ishwar Pawar / Adrian Pelin / Thomas H Pospiech / Cristina Puchades / Soumya Govinda Remesh / Maliheh Safari / Kaitlin Schaefer / Ming Sun / Mariano C Tabios / Aye C Thwin / Erron W Titus / Raphael Trenker / Eric Tse / Tsz Kin Martin Tsui / Feng Wang / Kaihua Zhang / Yang Zhang / Jianhua Zhao / Fengbo Zhou / Yuan Zhou / Lorena Zuliani-Alvarez / / David A Agard / Yifan Cheng / James S Fraser / Natalia Jura / Tanja Kortemme / Aashish Manglik / Daniel R Southworth / Robert M Stroud / Danielle L Swaney / Nevan J Krogan / Adam Frost / Oren S Rosenberg / Kliment A Verba / 要旨: The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic ...The SARS-CoV-2 protein Nsp2 has been implicated in a wide range of viral processes, but its exact functions, and the structural basis of those functions, remain unknown. Here, we report an atomic model for full-length Nsp2 obtained by combining cryo-electron microscopy with deep learning-based structure prediction from AlphaFold2. The resulting structure reveals a highly-conserved zinc ion-binding site, suggesting a role for Nsp2 in RNA binding. Mapping emerging mutations from variants of SARS-CoV-2 on the resulting structure shows potential host-Nsp2 interaction regions. Using structural analysis together with affinity tagged purification mass spectrometry experiments, we identify Nsp2 mutants that are unable to interact with the actin-nucleation-promoting WASH protein complex or with GIGYF2, an inhibitor of translation initiation and modulator of ribosome-associated quality control. Our work suggests a potential role of Nsp2 in linking viral transcription within the viral replication-transcription complexes (RTC) to the translation initiation of the viral message. Collectively, the structure reported here, combined with mutant interaction mapping, provides a foundation for functional studies of this evolutionary conserved coronavirus protein and may assist future drug design. | |||||||||||||||
履歴 |
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-構造の表示
ムービー |
ムービービューア |
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構造ビューア | EMマップ: SurfViewMolmilJmol/JSmol |
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_23970.map.gz | 78.3 MB | EMDBマップデータ形式 | |
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ヘッダ (付随情報) | emd-23970-v30.xml emd-23970.xml | 17.5 KB 17.5 KB | 表示 表示 | EMDBヘッダ |
FSC (解像度算出) | emd_23970_fsc.xml | 10 KB | 表示 | FSCデータファイル |
画像 | emd_23970.png | 41.7 KB | ||
マスクデータ | emd_23970_msk_1.map | 83.7 MB | マスクマップ | |
Filedesc metadata | emd-23970.cif.gz | 6.4 KB | ||
その他 | emd_23970_half_map_1.map.gz emd_23970_half_map_2.map.gz | 65.6 MB 65.4 MB | ||
アーカイブディレクトリ | http://ftp.pdbj.org/pub/emdb/structures/EMD-23970 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-23970 | HTTPS FTP |
-検証レポート
文書・要旨 | emd_23970_validation.pdf.gz | 915.1 KB | 表示 | EMDB検証レポート |
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文書・詳細版 | emd_23970_full_validation.pdf.gz | 914.7 KB | 表示 | |
XML形式データ | emd_23970_validation.xml.gz | 16.6 KB | 表示 | |
CIF形式データ | emd_23970_validation.cif.gz | 21.7 KB | 表示 | |
アーカイブディレクトリ | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23970 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-23970 | 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_23970.map.gz / 形式: CCP4 / 大きさ: 83.7 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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注釈 | SARS-CoV-2 Nsp2 main map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 0.834 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
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対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
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-添付データ
-マスク #1
ファイル | emd_23970_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 |
-ハーフマップ: SARS-CoV-2 Nsp2 half map - Odd
ファイル | emd_23970_half_map_1.map | ||||||||||||
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注釈 | SARS-CoV-2 Nsp2 half map - Odd | ||||||||||||
投影像・断面図 |
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密度ヒストグラム |
-ハーフマップ: SARS-CoV-2 Nsp2 half map - Even
ファイル | emd_23970_half_map_2.map | ||||||||||||
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注釈 | SARS-CoV-2 Nsp2 half map - Even | ||||||||||||
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 Nsp2
全体 | 名称: SARS-CoV-2 Nsp2 |
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要素 |
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-超分子 #1: SARS-CoV-2 Nsp2
超分子 | 名称: SARS-CoV-2 Nsp2 / タイプ: complex / ID: 1 / 親要素: 0 / 含まれる分子: #1 |
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由来(天然) | 生物種: Severe acute respiratory syndrome coronavirus 2 (ウイルス) |
分子量 | 理論値: 71 KDa |
-分子 #1: Non-structural protein 2
分子 | 名称: Non-structural protein 2 / タイプ: protein_or_peptide / ID: 1 / コピー数: 1 / 光学異性体: LEVO |
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由来(天然) | 生物種: Severe acute respiratory syndrome coronavirus 2 (ウイルス) |
分子量 | 理論値: 70.590219 KDa |
組換発現 | 生物種: Escherichia coli BL21(DE3) (大腸菌) |
配列 | 文字列: AYTRYVDNNF CGPDGYPLEC IKDLLARAGK ASCTLSEQLD FIDTKRGVYC CREHEHEIAW YTERSEKSYE LQTPFEIKLA KKFDTFNGE CPNFVFPLNS IIKTIQPRVE KKKLDGFMGR IRSVYPVASP NECNQMCLST LMKCDHCGET SWQTGDFVKA T CEFCGTEN ...文字列: AYTRYVDNNF CGPDGYPLEC IKDLLARAGK ASCTLSEQLD FIDTKRGVYC CREHEHEIAW YTERSEKSYE LQTPFEIKLA KKFDTFNGE CPNFVFPLNS IIKTIQPRVE KKKLDGFMGR IRSVYPVASP NECNQMCLST LMKCDHCGET SWQTGDFVKA T CEFCGTEN LTKEGATTCG YLPQNAVVKI YCPACHNSEV GPEHSLAEYH NESGLKTILR KGGRTIAFGG CVFSYVGCHN KC AYWVPRA SANIGCNHTG VVGEGSEGLN DNLLEILQKE KVNINIVGDF KLNEEIAIIL ASFSASTSAF VETVKGLDYK AFK QIVESC GNFKVTKGKA KKGAWNIGEQ KSILSPLYAF ASEAARVVRS IFSRTLETAQ NSVRVLQKAA ITILDGISQY SLRL IDAMM FTSDLATNNL VVMAYITGGV VQLTSQWLTN IFGTVYEKLK PVLDWLEEKF KEGVEFLRDG WEIVKFISTC ACEIV GGQI VTCAKEIKES VQTFFKLVNK FLALCADSII IGGAKLKALN LGETFVTHSK GLYRKCVKSR EETGLLMPLK APKEII FLE GETLPTEVLT EEVVLKTGDL QPLEQPTSEA VEAPLVGTPV CINGLMLLEI KDTEKYCALA PNMMVTNNTF TLKGG UniProtKB: Replicase polyprotein 1ab |
-分子 #2: ZINC ION
分子 | 名称: ZINC ION / タイプ: ligand / ID: 2 / コピー数: 3 / 式: ZN |
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分子量 | 理論値: 65.409 Da |
-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
濃度 | 0.42 mg/mL | ||||||||||||
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緩衝液 | pH: 8 構成要素:
詳細: Filtered and degassed before running FPLC | ||||||||||||
グリッド | モデル: Quantifoil R1.2/1.3 / 材質: GOLD / メッシュ: 400 / 支持フィルム - 材質: CARBON / 支持フィルム - トポロジー: HOLEY / 前処理 - タイプ: GLOW DISCHARGE / 前処理 - 時間: 30 sec. | ||||||||||||
凍結 | 凍結剤: ETHANE / チャンバー内湿度: 100 % / チャンバー内温度: 277.15 K / 装置: FEI VITROBOT MARK IV 詳細: Blot for 5 seconds before plunging into liquid ethane. | ||||||||||||
詳細 | This sample was monodisperse |
-電子顕微鏡法
顕微鏡 | FEI TITAN KRIOS |
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特殊光学系 | エネルギーフィルター - 名称: GIF Bioquantum / エネルギーフィルター - スリット幅: 20 eV |
撮影 | フィルム・検出器のモデル: GATAN K3 (6k x 4k) / 平均電子線量: 66.0 e/Å2 詳細: Two datasets comprising of 804 and 1116 118-frame super-resolution movies each were collected with a 3x3 image shift at a magnification of 105,000x with physical pixel size of 0.834 ang/pix ...詳細: Two datasets comprising of 804 and 1116 118-frame super-resolution movies each were collected with a 3x3 image shift at a magnification of 105,000x with physical pixel size of 0.834 ang/pix on a Titan Krios (ThermoFisher) equipped with a K3 camera and a Bioquantum energy filter (Gatan) set to a slit width of 20 eV. Collection dose rate was 8 e-/pixel/second for a total dose of 66 e-/ang^2. Defocus range was 0.8 to 2.4 micron. Each collection was performed with semi-automated scripts in SerialEM. |
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 / 倍率(公称値): 105000 |
試料ステージ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER ホルダー冷却材: NITROGEN |
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |