+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 6lnu | ||||||||||||
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タイトル | Cryo-EM structure of immature Zika virus | ||||||||||||
要素 | (Genome polyprotein) x 2 | ||||||||||||
キーワード | VIRUS / immature Zika virus / flavivirus | ||||||||||||
機能・相同性 | 機能・相同性情報 symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / negative regulation of innate immune response / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 4 iron, 4 sulfur cluster binding / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / molecular adaptor activity / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / centrosome / lipid binding / viral envelope / host cell nucleus / GTP binding / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding 類似検索 - 分子機能 | ||||||||||||
生物種 | Zika virus (ジカ熱ウイルス) | ||||||||||||
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: 9 Å | ||||||||||||
データ登録者 | Tan, T.Y. / Fibriansah, G. / Kostyuchenko, V.A. / Ng, T.S. / Lim, X.X. / Lim, X.N. / Shi, J. / Morais, M.C. / Corti, D. / Lok, S.M. | ||||||||||||
資金援助 | シンガポール, 3件
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引用 | ジャーナル: Nat Commun / 年: 2020 タイトル: Capsid protein structure in Zika virus reveals the flavivirus assembly process. 著者: Ter Yong Tan / Guntur Fibriansah / Victor A Kostyuchenko / Thiam-Seng Ng / Xin-Xiang Lim / Shuijun Zhang / Xin-Ni Lim / Jiaqi Wang / Jian Shi / Marc C Morais / Davide Corti / Shee-Mei Lok / 要旨: Structures of flavivirus (dengue virus and Zika virus) particles are known to near-atomic resolution and show detailed structure and arrangement of their surface proteins (E and prM in immature virus ...Structures of flavivirus (dengue virus and Zika virus) particles are known to near-atomic resolution and show detailed structure and arrangement of their surface proteins (E and prM in immature virus or M in mature virus). By contrast, the arrangement of the capsid proteins:RNA complex, which forms the core of the particle, is poorly understood, likely due to inherent dynamics. Here, we stabilize immature Zika virus via an antibody that binds across the E and prM proteins, resulting in a subnanometer resolution structure of capsid proteins within the virus particle. Fitting of the capsid protein into densities shows the presence of a helix previously thought to be removed via proteolysis. This structure illuminates capsid protein quaternary organization, including its orientation relative to the lipid membrane and the genomic RNA, and its interactions with the transmembrane regions of the surface proteins. Results show the capsid protein plays a central role in the flavivirus assembly process. | ||||||||||||
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 | 6lnu.cif.gz | 70.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb6lnu.ent.gz | 43.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 6lnu.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 | 6lnu_validation.pdf.gz | 947.1 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 6lnu_full_validation.pdf.gz | 946.7 KB | 表示 | |
XML形式データ | 6lnu_validation.xml.gz | 30.2 KB | 表示 | |
CIF形式データ | 6lnu_validation.cif.gz | 45.4 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ln/6lnu ftp://data.pdbj.org/pub/pdb/validation_reports/ln/6lnu | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
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対称性 | 点対称性: (シェーンフリース記号: I (正20面体型対称)) |
-要素
#1: タンパク質 | 分子量: 54444.051 Da / 分子数: 3 / 由来タイプ: 天然 由来: (天然) Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013) (ジカ熱ウイルス) 株: isolate ZIKV/Human/French Polynesia/10087PF/2013 参照: UniProt: A0A024B7W1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase #2: タンパク質 | 分子量: 18561.266 Da / 分子数: 3 / 由来タイプ: 天然 由来: (天然) Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013) (ジカ熱ウイルス) 株: isolate ZIKV/Human/French Polynesia/10087PF/2013 参照: UniProt: A0A024B7W1, flavivirin, nucleoside-triphosphate phosphatase, RNA helicase, mRNA (guanine-N7)-methyltransferase, methyltransferase cap1, RNA-directed RNA polymerase |
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-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: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 タイプ: VIRUS 詳細: The virus was isolated from Zika patient. The immature Zika virus was grown in Aedes Albopictus clone C6/36 cell. Entity ID: all / 由来: NATURAL |
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分子量 | 単位: MEGADALTONS / 実験値: NO |
由来(天然) | 生物種: Zika virus ZIKV/H. sapiens/FrenchPolynesia/10087PF/2013 (ジカ熱ウイルス) 株: H/PF/2013 |
ウイルスについての詳細 | 中空か: NO / エンベロープを持つか: YES / 単離: STRAIN / タイプ: VIRION |
緩衝液 | pH: 8 / 詳細: 10 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA, pH 8 |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES 詳細: the virus sample was incubated at 37deg C for 30 min prior to sample blotting onto the grid. |
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: SPOT SCAN |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 59000 X / 最大 デフォーカス(公称値): 3500 nm / 最小 デフォーカス(公称値): 500 nm / Cs: 2.7 mm |
撮影 | 電子線照射量: 18 e/Å2 フィルム・検出器のモデル: FEI FALCON II (4k x 4k) |
-解析
EMソフトウェア |
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CTF補正 | タイプ: PHASE FLIPPING ONLY | |||||||||||||||||||||||||||||||||||||||||||||
対称性 | 点対称性: I (正20面体型対称) | |||||||||||||||||||||||||||||||||||||||||||||
3次元再構成 | 解像度: 9 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 7922 / 対称性のタイプ: POINT | |||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | プロトコル: FLEXIBLE FIT | |||||||||||||||||||||||||||||||||||||||||||||
原子モデル構築 | PDB-ID: 4B03 Accession code: 4B03 / Source name: PDB / タイプ: experimental model |