+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1p58 | ||||||
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タイトル | Complex Organization of Dengue Virus Membrane Proteins as Revealed by 9.5 Angstrom Cryo-EM reconstruction | ||||||
要素 |
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キーワード | VIRUS / FLAVIVIRUS / FLAVIVIRIDAE / DENGUE VIRUS / GLYCOPROTEIN E FROM TICK-BORNE ENCEPHALITIS VIRUS / MEMBRANE PROTEIN M / CRYO-EM / Icosahedral virus | ||||||
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 / nucleoside-triphosphate phosphatase / protein complex oligomerization ...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 / 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 / host cell endoplasmic reticulum membrane / protein dimerization activity / 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 / 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 Puerto Rico/PR159-S1/1969 (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: 9.5 Å | ||||||
データ登録者 | Zhang, W. / Chipman, P.R. / Corver, J. / Johnson, P.R. / Zhang, Y. / Mukhopadhyay, S. / Baker, T.S. / Strauss, J.H. / Rossmann, M.G. / Kuhn, R.J. | ||||||
引用 | ジャーナル: Nat Struct Biol / 年: 2003 タイトル: Visualization of membrane protein domains by cryo-electron microscopy of dengue virus. 著者: Wei Zhang / Paul R Chipman / Jeroen Corver / Peter R Johnson / Ying Zhang / Suchetana Mukhopadhyay / Timothy S Baker / James H Strauss / Michael G Rossmann / Richard J Kuhn / 要旨: Improved technology for reconstructing cryo-electron microscopy (cryo-EM) images has now made it possible to determine secondary structural features of membrane proteins in enveloped viruses. The ...Improved technology for reconstructing cryo-electron microscopy (cryo-EM) images has now made it possible to determine secondary structural features of membrane proteins in enveloped viruses. The structure of mature dengue virus particles was determined to a resolution of 9.5 A by cryo-EM and image reconstruction techniques, establishing the secondary structural disposition of the 180 envelope (E) and 180 membrane (M) proteins in the lipid envelope. The alpha-helical 'stem' regions of the E molecules, as well as part of the N-terminal section of the M proteins, are buried in the outer leaflet of the viral membrane. The 'anchor' regions of E and the M proteins each form antiparallel E-E and M-M transmembrane alpha-helices, leaving their C termini on the exterior of the viral membrane, consistent with the predicted topology of the unprocessed polyprotein. This is one of only a few determinations of the disposition of transmembrane proteins in situ and shows that the nucleocapsid core and envelope proteins do not have a direct interaction in the mature virus. #1: ジャーナル: Cell(Cambridge,Mass.) / 年: 2002 タイトル: Structure of Dengue Virus: Implications for Flaviviruses Organization, Maturation and Fusion 著者: Kuhn, R.J. / Zhang, W. / Rossmann, M.G. / Pletnev, S.V. / Corver, J. / Lenches, E. / Jones, C.T. / Mukhopadhyay, S. / Chipman, P.R. / Strauss, E.G. / Baker, T.S. / Strauss, J.H. #2: ジャーナル: Nature / 年: 1995 タイトル: The envelope glycoprotein from tick-borne encephalitis virus at 2 A resolution 著者: Rey, F.A. / Heinz, F.X. / Mandl, C. / Kunz, C. / Harrison, S.C. #3: ジャーナル: Nature / 年: 1995 タイトル: Virology. When it's better to lie low. 著者: Kuhn, R.J. / Rossmann, M.G. #4: ジャーナル: Microbiol.Mol.Biol.Rev. / 年: 1999 タイトル: Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs 著者: Baker, T.S. / Olson, N.H. / Fuller, S.D. | ||||||
履歴 |
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Remark 999 | SEQUENCE Only coordinates for CA atoms were submitted. The deposited sequence is based on the E ...SEQUENCE Only coordinates for CA atoms were submitted. The deposited sequence is based on the E protein of dengue 2 virus S1 strain supplied by Hawaii Biotechnology Group, Inc. (Aiea, Hawaii). |
-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 | 1p58.cif.gz | 64.7 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1p58.ent.gz | 40.7 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1p58.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 | 1p58_validation.pdf.gz | 304.9 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1p58_full_validation.pdf.gz | 304.8 KB | 表示 | |
XML形式データ | 1p58_validation.xml.gz | 1.1 KB | 表示 | |
CIF形式データ | 1p58_validation.cif.gz | 15.3 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/p5/1p58 ftp://data.pdbj.org/pub/pdb/validation_reports/p5/1p58 | HTTPS FTP |
-関連構造データ
関連構造データ | |
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類似構造データ |
-リンク
-集合体
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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: 54401.758 Da / 分子数: 3 / 由来タイプ: 天然 由来: (天然) Dengue virus 2 Puerto Rico/PR159-S1/1969 (デング熱ウイルス) 属: Flavivirus / 生物種: Dengue virus / 株: PR159/S1 / 参照: UniProt: P12823, UniProt: P14337*PLUS #2: タンパク質 | 分子量: 8387.841 Da / 分子数: 3 / 由来タイプ: 天然 由来: (天然) Dengue virus 2 Puerto Rico/PR159-S1/1969 (デング熱ウイルス) 属: Flavivirus / 生物種: Dengue virus / 株: PR159/S1 / 参照: UniProt: P12823, UniProt: Q9WDA7*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 / 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: INVERTEBRATES / 単離: STRAIN / タイプ: VIRION |
天然宿主 | 生物種: Aedes aegypti / 株: C6/36 |
緩衝液 | 名称: 50 mM TRIS, 75 mM NaCl, 1 mM EDTA / pH: 7.6 / 詳細: 50 mM TRIS, 75 mM NaCl, 1 mM EDTA |
試料 | 濃度: 20 mg/ml / 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
試料支持 | 詳細: Concentration is given in PFU/ML |
急速凍結 | 詳細: SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE |
結晶化 | *PLUS 手法: 電子顕微鏡法 / 詳細: Electron Microscopy |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI/PHILIPS CM200T / 日付: 2000年6月27日 |
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電子銃 | 電子線源: FIELD EMISSION GUN / 加速電圧: 200 kV / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD / 倍率(公称値): 50000 X / 最大 デフォーカス(公称値): 4800 nm / 最小 デフォーカス(公称値): 800 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: FOURIER-BESSEL METHOD / 解像度: 9.5 Å / 粒子像の数: 1691 / ピクセルサイズ(公称値): 2.8 Å 詳細: THE RECONSTRUCTION WAS COMPUTED FROM 1691 DENGUE VIRUS IMAGES THAT WERE SELECTED FROM 78 MICROGRAPHS. ORIENTATIONS WERE DETERMINED BY THE MODEL-BASED POLAR-FOURIER TRANSFORM METHOD (BAKER AND ...詳細: THE RECONSTRUCTION WAS COMPUTED FROM 1691 DENGUE VIRUS IMAGES THAT WERE SELECTED FROM 78 MICROGRAPHS. ORIENTATIONS WERE DETERMINED BY THE MODEL-BASED POLAR-FOURIER TRANSFORM METHOD (BAKER AND CHENG, 1996, J.STRUC.BIOL. 116,120-130) AND REFINED BY THE MODEL-BASED FOURIER TRANSFORM REFINEMENT PROCEDURE(http://bond.cs.ucf.edu/ComputationalBiology/Projects/POR/Home.html). 対称性のタイプ: POINT | |||||||||||||||||||||
原子モデル構築 | 空間: REAL | |||||||||||||||||||||
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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