+
データを開く
-
基本情報
登録情報 | データベース: EMDB / ID: EMD-1167 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
タイトル | Cryo-EM reconstruction of dengue virus in complex with the carbohydrate recognition domain of DC-SIGN. | |||||||||
![]() | Map representing the difference between reconstructions of dengue virus in complex with CRD domain of DC-SIGN and dengue virus alone. Shows CRDs. | |||||||||
![]() |
| |||||||||
機能・相同性 | ![]() B cell adhesion / cell-cell recognition / modulation by virus of host process / intracellular transport of virus / peptide antigen transport / Butyrophilin (BTN) family interactions / fucose binding / positive regulation of viral life cycle / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ...B cell adhesion / cell-cell recognition / modulation by virus of host process / intracellular transport of virus / peptide antigen transport / Butyrophilin (BTN) family interactions / fucose binding / positive regulation of viral life cycle / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / regulation of T cell proliferation / RSV-host interactions / stimulatory C-type lectin receptor signaling pathway / antigen processing and presentation / D-mannose binding / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / positive regulation of T cell proliferation / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / CD209 (DC-SIGN) signaling / ribonucleoside triphosphate phosphatase activity / viral genome replication / endocytosis / peptide antigen binding / host cell / double-stranded RNA binding / viral capsid / protein complex oligomerization / monoatomic ion channel activity / virus receptor activity / carbohydrate binding / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / adaptive immune response / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / membrane => GO:0016020 / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / intracellular signal transduction / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont entry into host cell / induction by virus of host autophagy / immune response / external side of plasma membrane / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / innate immune response / 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 / cell surface / proteolysis / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane / cytoplasm 類似検索 - 分子機能 | |||||||||
生物種 | ![]() ![]() | |||||||||
手法 | 単粒子再構成法 / クライオ電子顕微鏡法 / 解像度: 25.0 Å | |||||||||
![]() | Pokidysheva E / Zhang Y / Battisti AJ / Bator-Kelly CM / Chipman PR / Xiao C / Gregorio GG / Hendrickson WA / Kuhn RJ / Rossmann MG | |||||||||
![]() | ![]() タイトル: Cryo-EM reconstruction of dengue virus in complex with the carbohydrate recognition domain of DC-SIGN. 著者: Elena Pokidysheva / Ying Zhang / Anthony J Battisti / Carol M Bator-Kelly / Paul R Chipman / Chuan Xiao / G Glenn Gregorio / Wayne A Hendrickson / Richard J Kuhn / Michael G Rossmann / ![]() 要旨: Dengue virus (DENV) is a significant human pathogen that causes millions of infections and results in about 24,000 deaths each year. Dendritic cell-specific ICAM3 grabbing nonintegrin (DC-SIGN), ...Dengue virus (DENV) is a significant human pathogen that causes millions of infections and results in about 24,000 deaths each year. Dendritic cell-specific ICAM3 grabbing nonintegrin (DC-SIGN), abundant in immature dendritic cells, was previously reported as being an ancillary receptor interacting with the surface of DENV. The structure of DENV in complex with the carbohydrate recognition domain (CRD) of DC-SIGN was determined by cryo-electron microscopy at 25 A resolution. One CRD monomer was found to bind to two glycosylation sites at Asn67 of two neighboring glycoproteins in each icosahedral asymmetric unit, leaving the third Asn67 residue vacant. The vacancy at the third Asn67 site is a result of the nonequivalence of the glycoprotein environments, leaving space for the primary receptor binding to domain III of E. The use of carbohydrate moieties for receptor binding sites suggests a mechanism for avoiding immune surveillance. | |||||||||
履歴 |
|
-
構造の表示
ムービー |
![]() |
---|---|
構造ビューア | EMマップ: ![]() ![]() ![]() |
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 | ![]() | 6.7 MB | ![]() | |
---|---|---|---|---|
ヘッダ (付随情報) | ![]() ![]() | 11.4 KB 11.4 KB | 表示 表示 | ![]() |
画像 | ![]() | 8.2 KB | ||
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-検証レポート
文書・要旨 | ![]() | 206.9 KB | 表示 | ![]() |
---|---|---|---|---|
文書・詳細版 | ![]() | 206.1 KB | 表示 | |
XML形式データ | ![]() | 4.4 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
関連構造データ | ![]() 2b6bMC ![]() 1166C M: このマップから作成された原子モデル C: 同じ文献を引用 ( |
---|---|
類似構造データ | 類似検索 - 機能・相同性 ![]() |
-
リンク
EMDBのページ | ![]() ![]() |
---|---|
「今月の分子」の関連する項目 |
-
マップ
ファイル | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
注釈 | Map representing the difference between reconstructions of dengue virus in complex with CRD domain of DC-SIGN and dengue virus alone. Shows CRDs. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
ボクセルのサイズ | X=Y=Z: 4.24 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
密度 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
対称性 | 空間群: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
詳細 | EMDB XML:
CCP4マップ ヘッダ情報:
|
-添付データ
-
試料の構成要素
-全体 : Dengue virus complexed with CRD domain of DC-SIGN
全体 | 名称: Dengue virus complexed with CRD domain of DC-SIGN |
---|---|
要素 |
|
-超分子 #1000: Dengue virus complexed with CRD domain of DC-SIGN
超分子 | 名称: Dengue virus complexed with CRD domain of DC-SIGN / タイプ: sample / ID: 1000 / 詳細: Calcium should be present in the sample. 集合状態: one monomer of CRD binds per virus icosahedral unit Number unique components: 2 |
---|---|
分子量 | 理論値: 12 MDa |
-超分子 #1: Dengue virus 2
超分子 | 名称: Dengue virus 2 / タイプ: virus / ID: 1 / NCBI-ID: 11060 / 生物種: Dengue virus 2 / ウイルスタイプ: VIRION / ウイルス・単離状態: STRAIN / ウイルス・エンベロープ: Yes / ウイルス・中空状態: No |
---|---|
宿主 | 生物種: ![]() |
分子量 | 実験値: 11 MDa / 理論値: 11 MDa |
-分子 #1: CRD domain of DC-SIGN
分子 | 名称: CRD domain of DC-SIGN / タイプ: protein_or_peptide / ID: 1 / 集合状態: monomer / 組換発現: Yes |
---|---|
由来(天然) | 生物種: ![]() |
分子量 | 実験値: 18 KDa / 理論値: 18 KDa |
組換発現 | 生物種: ![]() ![]() |
-実験情報
-構造解析
手法 | クライオ電子顕微鏡法 |
---|---|
![]() | 単粒子再構成法 |
試料の集合状態 | particle |
-
試料調製
濃度 | 2 mg/mL |
---|---|
緩衝液 | pH: 7.5 / 詳細: 50mM Tris 50mM NaCl 0.5 mM EDTA, 5 mM CaCl2, pH 7.5 |
グリッド | 詳細: 400 mesh copper grid |
凍結 | 凍結剤: ETHANE / 装置: HOMEMADE PLUNGER 詳細: Vitrification instrument: Guillotine-style plunge freezeing device 手法: Small aliquots of sample were applied to 400 mesh copper grids coated with holey carbon film and rapidly frozen by plunging into an ethane slush |
-
電子顕微鏡法
顕微鏡 | FEI/PHILIPS CM300FEG/T |
---|---|
温度 | 平均: 103 K |
アライメント法 | Legacy - 非点収差: objective lens astigmatism was corrected at 98,000 times magnification |
日付 | 2004年11月15日 |
撮影 | カテゴリ: FILM / フィルム・検出器のモデル: KODAK SO-163 FILM / デジタル化 - スキャナー: ZEISS SCAI / デジタル化 - サンプリング間隔: 7 µm / 実像数: 45 / 平均電子線量: 11.8 e/Å2 / Od range: 1.1 / ビット/ピクセル: 8 |
電子線 | 加速電圧: 300 kV / 電子線源: ![]() |
電子光学系 | 倍率(補正後): 33000 / 照射モード: OTHER / 撮影モード: BRIGHT FIELD / Cs: 2.0 mm / 最大 デフォーカス(公称値): 3.0 µm / 最小 デフォーカス(公称値): 1.0 µm / 倍率(公称値): 33000 |
試料ステージ | 試料ホルダー: Cryo / 試料ホルダーモデル: GATAN LIQUID NITROGEN |
-
画像解析
最終 再構成 | 想定した対称性 - 点群: I (正20面体型対称) / 解像度のタイプ: BY AUTHOR / 解像度: 25.0 Å / 解像度の算出法: FSC 0.5 CUT-OFF / 使用した粒子像数: 830 |
---|