+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6kur | |||||||||
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タイトル | Structure of influenza D virus polymerase bound to vRNA promoter in Mode B conformation (Class B1) | |||||||||
要素 |
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キーワード | VIRAL PROTEIN/RNA / influenza D virus / polymerase / cryo-EM / VIRAL PROTEIN-RNA complex | |||||||||
機能・相同性 | 機能・相同性情報 symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / cap snatching / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / nucleotide binding ...symbiont-mediated suppression of host mRNA transcription via inhibition of RNA polymerase II activity / host cell mitochondrion / 7-methylguanosine mRNA capping / cap snatching / virion component / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / nucleotide binding / host cell nucleus / RNA binding 類似検索 - 分子機能 | |||||||||
生物種 | Influenza D virus (インフルエンザウイルス) synthetic construct (人工物) | |||||||||
手法 | 電子顕微鏡法 / 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 3.7 Å | |||||||||
データ登録者 | Peng, Q. / Peng, R. / Qi, J. / Gao, G.F. / Shi, Y. | |||||||||
資金援助 | 中国, 1件
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引用 | ジャーナル: Nat Microbiol / 年: 2019 タイトル: Structural insight into RNA synthesis by influenza D polymerase. 著者: Qi Peng / Yuqian Liu / Ruchao Peng / Min Wang / Wei Yang / Hao Song / Yuhai Chen / Sheng Liu / Min Han / Xinzheng Zhang / Peiyi Wang / Jinghua Yan / Buchang Zhang / Jianxun Qi / Tao Deng / ...著者: Qi Peng / Yuqian Liu / Ruchao Peng / Min Wang / Wei Yang / Hao Song / Yuhai Chen / Sheng Liu / Min Han / Xinzheng Zhang / Peiyi Wang / Jinghua Yan / Buchang Zhang / Jianxun Qi / Tao Deng / George F Gao / Yi Shi / 要旨: The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the ...The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the conserved viral genomic RNA (vRNA) or complementary RNA (cRNA) promoter. Here, we determined the apo and promoter-bound influenza D polymerase structures using cryo-electron microscopy and found the polymerase has an evolutionarily conserved stable core structure with inherently flexible peripheral domains. Strikingly, two conformations (mode A and B) of the vRNA promoter were observed where the 3'-vRNA end can bind at two different sites, whereas the cRNA promoter only binds in the mode B conformation. Functional studies confirmed the critical role of the mode B conformation for vRNA synthesis via the intermediate cRNA but not for cRNA production, which is mainly regulated by the mode A conformation. Both conformations participate in the regulation of the transcription process. This work advances our understanding of the regulatory mechanisms for the synthesis of different RNA species by influenza virus polymerase and opens new opportunities for antiviral drug design. #1: ジャーナル: Nat Microbiol / 年: 2019 タイトル: Structural insight into RNA synthesis by influenza D polymerase. 著者: Qi Peng / Yuqian Liu / Ruchao Peng / Min Wang / Wei Yang / Hao Song / Yuhai Chen / Sheng Liu / Min Han / Xinzheng Zhang / Peiyi Wang / Jinghua Yan / Buchang Zhang / Jianxun Qi / Tao Deng / ...著者: Qi Peng / Yuqian Liu / Ruchao Peng / Min Wang / Wei Yang / Hao Song / Yuhai Chen / Sheng Liu / Min Han / Xinzheng Zhang / Peiyi Wang / Jinghua Yan / Buchang Zhang / Jianxun Qi / Tao Deng / George F Gao / Yi Shi / 要旨: The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the ...The influenza virus polymerase uses capped RNA primers to initiate transcription, and a combination of terminal and internal de novo initiations for the two-step replication process by binding the conserved viral genomic RNA (vRNA) or complementary RNA (cRNA) promoter. Here, we determined the apo and promoter-bound influenza D polymerase structures using cryo-electron microscopy and found the polymerase has an evolutionarily conserved stable core structure with inherently flexible peripheral domains. Strikingly, two conformations (mode A and B) of the vRNA promoter were observed where the 3'-vRNA end can bind at two different sites, whereas the cRNA promoter only binds in the mode B conformation. Functional studies confirmed the critical role of the mode B conformation for vRNA synthesis via the intermediate cRNA but not for cRNA production, which is mainly regulated by the mode A conformation. Both conformations participate in the regulation of the transcription process. This work advances our understanding of the regulatory mechanisms for the synthesis of different RNA species by influenza virus polymerase and opens new opportunities for antiviral 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 | 分子: MolmilJmol/JSmol |
-ダウンロードとリンク
-ダウンロード
PDBx/mmCIF形式 | 6kur.cif.gz | 301.6 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6kur.ent.gz | 229.1 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6kur.json.gz | ツリー表示 | PDBx/mmJSON形式 | |
その他 | その他のダウンロード |
-検証レポート
文書・要旨 | 6kur_validation.pdf.gz | 779.5 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6kur_full_validation.pdf.gz | 792.3 KB | 表示 | |
XML形式データ | 6kur_validation.xml.gz | 46.3 KB | 表示 | |
CIF形式データ | 6kur_validation.cif.gz | 71.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ku/6kur ftp://data.pdbj.org/pub/pdb/validation_reports/ku/6kur | HTTPS FTP |
-関連構造データ
関連構造データ | 9581MC 9577C 9578C 9579C 9580C 9582C 9887C 9888C 6kujC 6kukC 6kupC 6kutC 6kuuC 6kuvC 6kv5C M: このデータのモデリングに利用したマップデータ C: 同じ文献を引用 (文献) |
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類似構造データ |
-リンク
-集合体
登録構造単位 |
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1 |
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-要素
#1: タンパク質 | 分子量: 83036.086 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Influenza D virus (D/swine/Oklahoma/1334/2011) (インフルエンザウイルス) 株: D/swine/Oklahoma/1334/2011 / 遺伝子: P3 発現宿主: Spodoptera aff. frugiperda 1 BOLD-2017 (蝶・蛾) 参照: UniProt: K9LHJ4 |
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#2: タンパク質 | 分子量: 86138.844 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Influenza D virus (D/swine/Oklahoma/1334/2011) (インフルエンザウイルス) 株: D/swine/Oklahoma/1334/2011 / 遺伝子: PB1 発現宿主: Spodoptera aff. frugiperda 1 BOLD-2017 (蝶・蛾) 参照: UniProt: K9LH03, RNA-directed RNA polymerase |
#3: タンパク質 | 分子量: 88480.484 Da / 分子数: 1 / 由来タイプ: 組換発現 由来: (組換発現) Influenza D virus (D/swine/Oklahoma/1334/2011) (インフルエンザウイルス) 株: D/swine/Oklahoma/1334/2011 / 遺伝子: PB2 発現宿主: Spodoptera aff. frugiperda 1 BOLD-2017 (蝶・蛾) 参照: UniProt: K9LHF3 |
#4: RNA鎖 | 分子量: 4337.563 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
#5: RNA鎖 | 分子量: 4918.042 Da / 分子数: 1 / 由来タイプ: 合成 / 由来: (合成) synthetic construct (人工物) |
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
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EM実験 | 試料の集合状態: PARTICLE / 3次元再構成法: 単粒子再構成法 |
-試料調製
構成要素 | 名称: Structure of influenza D virus polymerase bound to vRNA promoter in mode B conformation (class B1) タイプ: COMPLEX / Entity ID: all / 由来: RECOMBINANT |
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由来(天然) | 生物種: Influenza D virus (インフルエンザウイルス) |
由来(組換発現) | 生物種: Spodoptera aff. frugiperda 1 BOLD-2017 (蝶・蛾) |
緩衝液 | pH: 7.5 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
実験機器 | モデル: Titan Krios / 画像提供: FEI Company |
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顕微鏡 | モデル: FEI TITAN KRIOS |
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 40 e/Å2 フィルム・検出器のモデル: GATAN K2 QUANTUM (4k x 4k) |
-解析
ソフトウェア | 名称: PHENIX / バージョン: 1.11.1_2575: / 分類: 精密化 | ||||||||||||||||||||||||
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CTF補正 | タイプ: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
対称性 | 点対称性: C1 (非対称) | ||||||||||||||||||||||||
3次元再構成 | 解像度: 3.7 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 298468 / 対称性のタイプ: POINT | ||||||||||||||||||||||||
拘束条件 |
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