+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 2b6b | ||||||
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タイトル | Cryo EM structure of Dengue complexed with CRD of DC-SIGN | ||||||
要素 |
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キーワード | Virus/Receptor / Cryo EM dengue CRD DC-SIGN / Icosahedral virus / Virus-Receptor COMPLEX | ||||||
機能・相同性 | 機能・相同性情報 B cell adhesion / cell-cell recognition / peptide antigen transport / modulation by virus of host process / intracellular transport of virus / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / 宿主 / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules ...B cell adhesion / cell-cell recognition / peptide antigen transport / modulation by virus of host process / intracellular transport of virus / Butyrophilin (BTN) family interactions / positive regulation of viral life cycle / 宿主 / virion binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / regulation of T cell proliferation / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / stimulatory C-type lectin receptor signaling pathway / mannose binding / host cell mitochondrion / antigen processing and presentation / 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 / エンドサイトーシス / peptide antigen binding / カプシド / : / double-stranded RNA binding / virus receptor activity / protein complex oligomerization / monoatomic ion channel activity / carbohydrate binding / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / 獲得免疫系 / membrane => GO:0016020 / host cell endoplasmic reticulum membrane / protein dimerization activity / intracellular signal transduction / 免疫応答 / induction by virus of host autophagy / symbiont entry into host cell / viral RNA genome replication / external side of plasma membrane / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / 自然免疫系 / fusion of virus membrane with host endosome membrane / エンベロープ (ウイルス) / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / 細胞膜 / タンパク質分解 / extracellular region / ATP binding / 生体膜 / metal ion binding / 細胞膜 / 細胞質 類似検索 - 分子機能 | ||||||
生物種 | Homo sapiens (ヒト) Dengue virus (デング熱ウイルス) | ||||||
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: 25 Å | ||||||
データ登録者 | Pokidysheva, E. / Zhang, Y. / Battisti, A.J. / Bator-Kelly, C.M. / Chipman, P.R. / Gregorio, G. / Hendrickson, W.A. / Kuhn, R.J. / Rossmann, M.G. | ||||||
引用 | ジャーナル: Cell / 年: 2006 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 |
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Remark 999 | SEQUENCE The proteins in this entry contain CA only. |
-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 | 2b6b.cif.gz | 55.3 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb2b6b.ent.gz | 32.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 2b6b.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
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/b6/2b6b ftp://data.pdbj.org/pub/pdb/validation_reports/b6/2b6b | HTTPS FTP |
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-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: (ヘルマン・モーガン記号: 532 / 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: 43819.391 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Dengue virus (デング熱ウイルス) / 属: Flavivirus / 参照: GenBank: 323503, UniProt: Q9WDA7*PLUS #2: タンパク質 | | 分子量: 19920.029 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Homo sapiens (ヒト) / 遺伝子: CD209 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: Q96QQ4, UniProt: Q9NNX6*PLUS |
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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: DENGUE VIRUS COMPLEXED WITH CRD OF DC-SIGN / タイプ: VIRUS |
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ウイルスについての詳細 | ホストのカテゴリ: INSECT / タイプ: VIRION |
天然宿主 | 株: C6/36 |
緩衝液 | pH: 7.5 / 詳細: 50mM Tris 50mM NaCl 0.5 mM EDTA, 5 mM CaCl2, pH 7.5 |
試料 | 濃度: 20 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: SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI/PHILIPS CM300FEG/T / 日付: 2004年11月15日 |
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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 FIELDBright-field microscopy / 倍率(公称値): 50000 X / 最大 デフォーカス(公称値): 3000 nm / 最小 デフォーカス(公称値): 1100 nm / Cs: 2 mm |
試料ホルダ | 温度: 87 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 27 e/Å2 / フィルム・検出器のモデル: KODAK SO-163 FILM |
-解析
EMソフトウェア |
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CTF補正 | 詳細: EACH VIRAL IMAGE WAS CTF CORRECTED BEFORE RECONSTRUCTION, BASED ON THE FOLLOWING EQUATION: F(CORR)=F(OBS)/[|CTF|+WIENER*(1-|CTF|)] | |||||||||||||||||||||
対称性 | 点対称性: I (正20面体型対称) | |||||||||||||||||||||
3次元再構成 | 手法: MODEL-BASED / 解像度: 25 Å / 粒子像の数: 830 / ピクセルサイズ(公称値): 2.95 Å / 対称性のタイプ: POINT | |||||||||||||||||||||
原子モデル構築 | プロトコル: OTHER / 詳細: METHOD--PLEASE SEE CITATION | |||||||||||||||||||||
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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