+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3j0b | ||||||
---|---|---|---|---|---|---|---|
タイトル | cryo-EM reconstruction of West Nile virus | ||||||
要素 | envelope glycoprotein E | ||||||
キーワード | VIRUS / West Nile Virus | ||||||
機能・相同性 | 機能・相同性情報 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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase 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 / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / 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 / symbiont-mediated suppression of host innate immune response / induction by virus of host autophagy / symbiont entry into host cell / 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 / 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 | West Nile virus (西ナイルウイルス) | ||||||
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: 10.3 Å | ||||||
データ登録者 | Zhang, W. / Kaufmann, B. / Chipman, P.R. / Kuhn, R.J. / Rossmann, M.G. | ||||||
引用 | ジャーナル: J Struct Biol / 年: 2013 タイトル: Membrane curvature in flaviviruses. 著者: Wei Zhang / Bärbel Kaufmann / Paul R Chipman / Richard J Kuhn / Michael G Rossmann / 要旨: Coordinated interplay between membrane proteins and the lipid bilayer is required for such processes as transporter function and the entrance of enveloped viruses into host cells. In this study, ...Coordinated interplay between membrane proteins and the lipid bilayer is required for such processes as transporter function and the entrance of enveloped viruses into host cells. In this study, three-dimensional cryo-electron microscopy density maps of mature and immature flaviviruses were analyzed to assess the curvature of the membrane leaflets and its relation to membrane-bound viral glycoproteins. The overall morphology of the viral membrane is determined by the icosahedral scaffold composed of envelope (E) and membrane (M) proteins through interaction of the proteins' stem-anchor regions with the membrane. In localized regions, small membrane areas exhibit convex, concave, flat or saddle-shaped surfaces that are constrained by the specific protein organization within each membrane leaflet. These results suggest that the organization of membrane proteins in small enveloped viruses mediate the formation of membrane curvature. | ||||||
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 | 3j0b.cif.gz | 50.3 KB | 表示 | PDBx/mmCIF形式 |
---|---|---|---|---|
PDB形式 | pdb3j0b.ent.gz | 30 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3j0b.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 | 3j0b_validation.pdf.gz | 804.5 KB | 表示 | wwPDB検証レポート |
---|---|---|---|---|
文書・詳細版 | 3j0b_full_validation.pdf.gz | 806 KB | 表示 | |
XML形式データ | 3j0b_validation.xml.gz | 21.1 KB | 表示 | |
CIF形式データ | 3j0b_validation.cif.gz | 30.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/j0/3j0b ftp://data.pdbj.org/pub/pdb/validation_reports/j0/3j0b | 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: 43272.098 Da / 分子数: 3 / 断片: UNP residues 291-690 / 由来タイプ: 天然 / 由来: (天然) West Nile virus (西ナイルウイルス) / 参照: UniProt: Q9Q6P4 |
---|
-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: West Nile Virus / タイプ: VIRUS |
---|---|
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 |
緩衝液 | 名称: TNE (12 mM Tris, 120 mM NaCl, 1 mM EDTA) / pH: 8 / 詳細: 12 mM Tris-HCL, 120 mM NaCl, 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 / 詳細: 12 mM Tris-HCL, 120 mM NaCl, 1 mM EDTA |
試料支持 | 詳細: 400 mesh holey carbon copper grid |
急速凍結 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE / Temp: 98 K / 詳細: vitrification carried out in a BSL3 lab 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 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 means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be melted slightly. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot off 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 in 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: 2004年10月21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 / 倍率(補正後): 47440 X / 最大 デフォーカス(公称値): 321 nm / 最小 デフォーカス(公称値): 112 nm / Cs: 2 mm / 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 / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
撮影 | 電子線照射量: 30 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: 10.3 Å / 解像度の算出法: FSC 0.5 CUT-OFF / 粒子像の数: 1556 / 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: REAL / Target criteria: Cross-correlation coefficient / 詳細: REFINEMENT PROTOCOL--Rigid Body | ||||||||||||
原子モデル構築 | PDB-ID: 2HG0 Accession code: 2HG0 / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化ステップ | サイクル: LAST
|