+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j8d | ||||||
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タイトル | Cryoelectron microscopy of dengue-Fab E104 complex at pH 5.5 | ||||||
要素 |
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キーワード | VIRUS/IMMUNE SYSTEM / Dengue virus / DENV2 Fab E104 / Low pH / fusion trimer / VIRUS-IMMUNE SYSTEM complex | ||||||
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 / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / channel activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / monoatomic ion transmembrane transport ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / channel activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / monoatomic ion transmembrane transport / 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 / RNA helicase activity / host cell perinuclear region of cytoplasm / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / 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 / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding 類似検索 - 分子機能 | ||||||
生物種 | Dengue virus 2 Thailand/16681/84 (デング熱ウイルス) Mus musculus (ハツカネズミ) | ||||||
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: 26 Å | ||||||
データ登録者 | Zhang, X.Z. / Sheng, J. / Austin, S.K. / Hoornweg, T. / Smit, J.M. / Kuhn, R.J. / Diamond, M.S. / Rossmann, M.G. | ||||||
引用 | ジャーナル: J Virol / 年: 2015 タイトル: Structure of acidic pH dengue virus showing the fusogenic glycoprotein trimers. 著者: Xinzheng Zhang / Ju Sheng / S Kyle Austin / Tabitha E Hoornweg / Jolanda M Smit / Richard J Kuhn / Michael S Diamond / Michael G Rossmann / 要旨: Flaviviruses undergo large conformational changes during their life cycle. Under acidic pH conditions, the mature virus forms transient fusogenic trimers of E glycoproteins that engage the lipid ...Flaviviruses undergo large conformational changes during their life cycle. Under acidic pH conditions, the mature virus forms transient fusogenic trimers of E glycoproteins that engage the lipid membrane in host cells to initiate viral fusion and nucleocapsid penetration into the cytoplasm. However, the dynamic nature of the fusogenic trimer has made the determination of its structure a challenge. Here we have used Fab fragments of the neutralizing antibody DV2-E104 to stop the conformational change of dengue virus at an intermediate stage of the fusion process. Using cryo-electron microscopy, we show that in this intermediate stage, the E glycoproteins form 60 trimers that are similar to the predicted "open" fusogenic trimer. IMPORTANCE: The structure of a dengue virus has been captured during the formation of fusogenic trimers. This was accomplished by binding Fab fragments of the neutralizing antibody DV2-E104 to the ...IMPORTANCE: The structure of a dengue virus has been captured during the formation of fusogenic trimers. This was accomplished by binding Fab fragments of the neutralizing antibody DV2-E104 to the virus at neutral pH and then decreasing the pH to 5.5. These trimers had an "open" conformation, which is distinct from the "closed" conformation of postfusion trimers. Only two of the three E proteins within each spike are bound by a Fab molecule at domain III. Steric hindrance around the icosahedral 3-fold axes prevents binding of a Fab to the third domain III of each E protein spike. Binding of the DV2-E104 Fab fragments prevents domain III from rotating by about 130° to the postfusion orientation and thus precludes the stem region from "zipping" together the three E proteins along the domain II boundaries into the "closed" postfusion conformation, thus inhibiting fusion. | ||||||
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 | 3j8d.cif.gz | 82.2 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3j8d.ent.gz | 48.3 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3j8d.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 | 3j8d_validation.pdf.gz | 835.7 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3j8d_full_validation.pdf.gz | 836.4 KB | 表示 | |
XML形式データ | 3j8d_validation.xml.gz | 28.1 KB | 表示 | |
CIF形式データ | 3j8d_validation.cif.gz | 42.2 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j8/3j8d ftp://data.pdbj.org/pub/pdb/validation_reports/j8/3j8d | 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: 10616.091 Da / 分子数: 2 / 断片: SEE REMARK 999 / 由来タイプ: 組換発現 由来: (組換発現) Dengue virus 2 Thailand/16681/84 (デング熱ウイルス) 発現宿主: unidentified (未定義) / 参照: UniProt: P17763*PLUS #2: 抗体 | 分子量: 46637.730 Da / 分子数: 2 / 由来タイプ: 天然 / 由来: (天然) Mus musculus (ハツカネズミ) #3: タンパク質 | 分子量: 43819.391 Da / 分子数: 3 / 断片: UNP residues 281-674 / 由来タイプ: 組換発現 由来: (組換発現) Dengue virus 2 Thailand/16681/84 (デング熱ウイルス) 発現宿主: unidentified (未定義) / 参照: UniProt: P12823, UniProt: P29990*PLUS 配列の詳細 | THE MODELED SEQUENCE FOR GLYCOPROTE | |
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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 |
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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 / ホストのカテゴリ: VERTEBRATES / 単離: STRAIN / タイプ: VIRION | ||||||||||||||||||||
天然宿主 | 生物種: Homo sapiens | ||||||||||||||||||||
緩衝液 | 名称: 120 mM NaCl, 20 mM Tris HCl, 1 mM EDTA / pH: 5.5 / 詳細: 120 mM NaCl, 20 mM Tris HCl, 1 mM EDTA | ||||||||||||||||||||
試料 | 濃度: 1 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES | ||||||||||||||||||||
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE / 詳細: Plunged into liquid 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 / 日付: 2013年1月1日 |
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 / Cs: 2.7 mm / カメラ長: 0 mm |
試料ホルダ | 試料ホルダーモデル: FEI TITAN KRIOS AUTOGRID HOLDER |
撮影 | 電子線照射量: 24 e/Å2 フィルム・検出器のモデル: GATAN ULTRASCAN 4000 (4k x 4k) |
画像スキャン | デジタル画像の数: 1000 |
放射 | プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 相対比: 1 |
-解析
EMソフトウェア |
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対称性 | 点対称性: I (正20面体型対称) | |||||||||||||||||||||
3次元再構成 | 解像度: 26 Å / 解像度の算出法: FSC 0.143 CUT-OFF / 粒子像の数: 528 / ピクセルサイズ(公称値): 5.2 Å / ピクセルサイズ(実測値): 5.2 Å / 詳細: (Single particle--Applied symmetry: I) / 対称性のタイプ: POINT | |||||||||||||||||||||
原子モデル構築 | プロトコル: RIGID BODY FIT / 空間: RECIPROCAL / 詳細: REFINEMENT PROTOCOL--rigid body | |||||||||||||||||||||
原子モデル構築 |
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精密化ステップ | サイクル: LAST
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