+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1thd | ||||||
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タイトル | COMPLEX ORGANIZATION OF DENGUE VIRUS E PROTEIN AS REVEALED BY 9.5 ANGSTROM CRYO-EM RECONSTRUCTION | ||||||
要素 | Major envelope protein E | ||||||
キーワード | VIRUS / FLAVIVIRUS / FLAVIVIRIDAE / DENGUE VIRUS / GLYCOPROTEIN E / 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity ...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 / 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, Y. / Zhang, W. / Ogata, S. / Clements, D. / Strauss, J.H. / Baker, T.S. / Kuhn, R.J. / Rossmann, M.G. | ||||||
引用 | ジャーナル: Structure / 年: 2004 タイトル: Conformational changes of the flavivirus E glycoprotein. 著者: Ying Zhang / Wei Zhang / Steven Ogata / David Clements / James H Strauss / Timothy S Baker / Richard J Kuhn / Michael G Rossmann / 要旨: Dengue virus, a member of the Flaviviridae family, has a surface composed of 180 copies each of the envelope (E) glycoprotein and the membrane (M) protein. The crystal structure of an N-terminal ...Dengue virus, a member of the Flaviviridae family, has a surface composed of 180 copies each of the envelope (E) glycoprotein and the membrane (M) protein. The crystal structure of an N-terminal fragment of E has been determined and compared with a previously described structure. The primary difference between these structures is a 10 degrees rotation about a hinge relating the fusion domain DII to domains DI and DIII. These two rigid body components were used for independent fitting of E into the cryo-electron microscopy maps of both immature and mature dengue viruses. The fitted E structures in these two particles showed a difference of 27 degrees between the two components. Comparison of the E structure in its postfusion state with that in the immature and mature virions shows a rotation approximately around the same hinge. Flexibility of E is apparently a functional requirement for assembly and infection of flaviviruses. #1: 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. | ||||||
履歴 |
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Remark 999 | SEQUENCE AUTHORS SUBMITTED COORDINATES FOR CA ATOMS 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 | 1thd.cif.gz | 49.1 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1thd.ent.gz | 29.9 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1thd.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 | 1thd_validation.pdf.gz | 306.5 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1thd_full_validation.pdf.gz | 306 KB | 表示 | |
XML形式データ | 1thd_validation.xml.gz | 702 B | 表示 | |
CIF形式データ | 1thd_validation.cif.gz | 10.9 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/th/1thd ftp://data.pdbj.org/pub/pdb/validation_reports/th/1thd | HTTPS FTP |
-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: 43863.398 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 |
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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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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 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
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 |
-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 / 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.STRUCT.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 | プロトコル: OTHER / 詳細: METHOD--please see citation | ||||||||||||
原子モデル構築 | PDB-ID: 1TG8 Accession code: 1TG8 / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化ステップ | サイクル: LAST
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