+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3ixy | ||||||
---|---|---|---|---|---|---|---|
タイトル | The pseudo-atomic structure of dengue immature virus in complex with Fab fragments of the anti-fusion loop antibody E53 | ||||||
要素 |
| ||||||
キーワード | VIRUS / Dengue Virus / DENV / immature / fusion loop / Fab / E53 / ATP-binding / Envelope protein / Helicase / Hydrolase / Membrane / Nucleotide-binding / RNA replication / Transmembrane / Virion / Capsid protein / Cleavage on pair of basic residues / Core protein / Endoplasmic reticulum / Glycoprotein / Secreted | ||||||
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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding ...: / : / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / serine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding 類似検索 - 分子機能 | ||||||
生物種 | Dengue virus 2 (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: 23 Å | ||||||
データ登録者 | Cherrier, M.V. / Kaufmann, B. / Nybakken, G.E. / Lok, S.M. / Warren, J.T. / Nelson, C.A. / Kostyuchenko, V.A. / Holdaway, H.A. / Chipman, P.R. / Kuhn, R.J. ...Cherrier, M.V. / Kaufmann, B. / Nybakken, G.E. / Lok, S.M. / Warren, J.T. / Nelson, C.A. / Kostyuchenko, V.A. / Holdaway, H.A. / Chipman, P.R. / Kuhn, R.J. / Diamond, M.S. / Rossmann, M.G. / Fremont, D.H. | ||||||
引用 | ジャーナル: EMBO J / 年: 2009 タイトル: Structural basis for the preferential recognition of immature flaviviruses by a fusion-loop antibody. 著者: Mickaël V Cherrier / Bärbel Kaufmann / Grant E Nybakken / Shee-Mei Lok / Julia T Warren / Beverly R Chen / Christopher A Nelson / Victor A Kostyuchenko / Heather A Holdaway / Paul R Chipman ...著者: Mickaël V Cherrier / Bärbel Kaufmann / Grant E Nybakken / Shee-Mei Lok / Julia T Warren / Beverly R Chen / Christopher A Nelson / Victor A Kostyuchenko / Heather A Holdaway / Paul R Chipman / Richard J Kuhn / Michael S Diamond / Michael G Rossmann / Daved H Fremont / 要旨: Flaviviruses are a group of human pathogens causing severe encephalitic or hemorrhagic diseases that include West Nile, dengue and yellow fever viruses. Here, using X-ray crystallography we have ...Flaviviruses are a group of human pathogens causing severe encephalitic or hemorrhagic diseases that include West Nile, dengue and yellow fever viruses. Here, using X-ray crystallography we have defined the structure of the flavivirus cross-reactive antibody E53 that engages the highly conserved fusion loop of the West Nile virus envelope glycoprotein. Using cryo-electron microscopy, we also determined that E53 Fab binds preferentially to spikes in noninfectious, immature flavivirions but is unable to bind significantly to mature virions, consistent with the limited solvent exposure of the epitope. We conclude that the neutralizing impact of E53 and likely similar fusion-loop-specific antibodies depends on its binding to the frequently observed immature component of flavivirus particles. Our results elucidate how fusion-loop antibodies, which comprise a significant fraction of the humoral response against flaviviruses, can function to control infection without appreciably recognizing mature virions. As these highly cross-reactive antibodies are often weakly neutralizing they also may contribute to antibody-dependent enhancement and flavi virus pathogenesis thereby complicating development of safe and effective vaccines. | ||||||
履歴 |
|
-構造の表示
ムービー |
ムービービューア |
---|---|
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 | 3ixy.cif.gz | 87.3 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb3ixy.ent.gz | 54.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3ixy.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 | 3ixy_validation.pdf.gz | 823.5 KB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 3ixy_full_validation.pdf.gz | 823.8 KB | 表示 | |
XML形式データ | 3ixy_validation.xml.gz | 30.3 KB | 表示 | |
CIF形式データ | 3ixy_validation.cif.gz | 46.8 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/ix/3ixy ftp://data.pdbj.org/pub/pdb/validation_reports/ix/3ixy | HTTPS FTP |
-関連構造データ
-リンク
-集合体
登録構造単位 |
|
---|---|
1 |
| x 60
2 |
|
3 |
| x 5
4 |
| x 6
5 |
|
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: 43904.410 Da / 分子数: 3 / 由来タイプ: 組換発現 由来: (組換発現) Dengue virus 2 (デング熱ウイルス) 株: DENV2 / 細胞株 (発現宿主): C6/36 / 発現宿主: Aedes albopictus (ヒトスジシマカ) / 参照: UniProt: O11875, UniProt: Q9WDA6*PLUS #2: タンパク質 | 分子量: 9261.531 Da / 分子数: 3 / 由来タイプ: 組換発現 由来: (組換発現) Dengue virus 2 (デング熱ウイルス) 株: DENV2 / 細胞株 (発現宿主): C6/36 / 発現宿主: Aedes albopictus (ヒトスジシマカ) / 参照: UniProt: P18356 #3: 抗体 | 分子量: 23630.504 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): DE3 #4: 抗体 | 分子量: 23588.107 Da / 分子数: 2 / 由来タイプ: 組換発現 / 由来: (組換発現) Mus musculus (ハツカネズミ) / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): DE3 |
---|
-実験情報
-実験
実験 | 手法: 電子顕微鏡法 |
---|---|
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: Immature Dengue Virus complexed with E53 Fab / タイプ: VIRUS 詳細: T1 icosahedron with three E monomers and two Fab per asymmetric unit |
---|---|
分子量 | 値: 24.4 MDa / 実験値: NO |
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 | pH: 7.6 / 詳細: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA |
試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES / 詳細: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE 手法: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine ...手法: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope. |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI/PHILIPS CM300FEG/T / 日付: 2008年4月4日 / 詳細: low dose |
---|---|
電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 300 kV / 照射モード: FLOOD BEAM / Electron beam tilt params: 0 |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 45000 X / 倍率(補正後): 47244 X / 最大 デフォーカス(公称値): 2728 nm / 最小 デフォーカス(公称値): 1876 nm / Cs: 2 mm / 非点収差: live FFT / カメラ長: 0 mm |
試料ホルダ | 試料ホルダーモデル: GATAN LIQUID NITROGEN / 資料ホルダタイプ: EUCENTRIC / 温度: 98 K / 傾斜角・最大: -9999 ° / 傾斜角・最小: -9999 ° |
撮影 | 電子線照射量: 15 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
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 |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF補正 | 詳細: Each particle | |||||||||||||||||||||
対称性 | 点対称性: I (正20面体型対称) | |||||||||||||||||||||
3次元再構成 | 解像度: 23 Å / 解像度の算出法: FSC 0.5 CUT-OFF / 粒子像の数: 2741 / ピクセルサイズ(実測値): 2.69 Å / 倍率補正: 47244 詳細: ( Details about the particle: 400 mesh copper grid ) 対称性のタイプ: POINT | |||||||||||||||||||||
原子モデル構築 |
| |||||||||||||||||||||
原子モデル構築 |
| |||||||||||||||||||||
精密化ステップ | サイクル: LAST
|