+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 1na4 | ||||||
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タイトル | The structure of immature Yellow Fever virus particle | ||||||
要素 | major envelope protein E | ||||||
キーワード | VIRUS / flavivirus / flaviviridae / yellow fever immature virus / prM particle / Icosahedral 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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-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 / viral capsid / double-stranded RNA binding / nucleoside-triphosphate phosphatase / 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 innate immune response / 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 | Yellow fever virus (黄熱ウイルス) | ||||||
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 | ||||||
データ登録者 | Zhang, Y. / Corver, J. / Chipman, P.R. / Lenches, E. / Zhang, W. / Pletnev, S.V. / Sedlak, D. / Baker, T.S. / Strauss, J.H. / Kuhn, R.J. / Rossmann, M.G. | ||||||
引用 | ジャーナル: EMBO J / 年: 2003 タイトル: Structures of immature flavivirus particles. 著者: Ying Zhang / Jeroen Corver / Paul R Chipman / Wei Zhang / Sergei V Pletnev / Dagmar Sedlak / Timothy S Baker / James H Strauss / Richard J Kuhn / Michael G Rossmann / 要旨: Structures of prM-containing dengue and yellow fever virus particles were determined to 16 and 25 A resolution, respectively, by cryoelectron microscopy and image reconstruction techniques. The ...Structures of prM-containing dengue and yellow fever virus particles were determined to 16 and 25 A resolution, respectively, by cryoelectron microscopy and image reconstruction techniques. The closely similar structures show 60 icosahedrally organized trimeric spikes on the particle surface. Each spike consists of three prM:E heterodimers, where E is an envelope glycoprotein and prM is the precursor to the membrane protein M. The pre-peptide components of the prM proteins in each spike cover the fusion peptides at the distal ends of the E glycoproteins in a manner similar to the organization of the glycoproteins in the alphavirus spikes. Each heterodimer is associated with an E and a prM transmembrane density. These transmembrane densities represent either an EE or prMprM antiparallel coiled coil by which each protein spans the membrane twice, leaving the C-terminus of each protein on the exterior of the viral membrane, consistent with the predicted membrane-spanning domains of the unprocessed polyprotein. | ||||||
履歴 |
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Remark 999 | SEQUENCE AUTHORS PROVIDED COORDINATES FOR ALPHA CARBONS ONLY. THE SEQRES RECORDS ARE FROM TICK-BORN ...SEQUENCE AUTHORS PROVIDED COORDINATES FOR ALPHA CARBONS ONLY. THE SEQRES RECORDS ARE FROM TICK-BORN ENCEPHALITIS VIRUS BECAUSE THE FITTING MODEL OF MAJOR ENVELOPE PROTEIN E (1SVB) WAS USED IN THIS STUDY. |
-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 | 1na4.cif.gz | 48.9 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb1na4.ent.gz | 29.8 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 1na4.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 | 1na4_validation.pdf.gz | 279 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 1na4_full_validation.pdf.gz | 278.6 KB | 表示 | |
XML形式データ | 1na4_validation.xml.gz | 874 B | 表示 | |
CIF形式データ | 1na4_validation.cif.gz | 11.1 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/na/1na4 ftp://data.pdbj.org/pub/pdb/validation_reports/na/1na4 | 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: 43231.145 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Yellow fever virus (黄熱ウイルス) / 属: Flavivirus / 参照: UniProt: P14336 |
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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: Yellow fever immature virus / タイプ: VIRUS 詳細: The samples were produced by adding ammonium chloride to the medium in the late infection stage. |
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試料 | 包埋: NO / シャドウイング: NO / 染色: NO / 凍結: YES |
急速凍結 | 凍結剤: ETHANE |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI/PHILIPS CM300FEG/T |
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電子銃 | 電子線源: FIELD EMISSION GUN / 照射モード: FLOOD BEAM |
電子レンズ | モード: BRIGHT FIELD |
撮影 | 電子線照射量: 15 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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対称性 | 点対称性: I (正20面体型対称) | ||||||||||||
3次元再構成 | 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 | PDB-ID: 1SVB Accession code: 1SVB / Source name: PDB / タイプ: experimental model | ||||||||||||
精密化ステップ | サイクル: LAST
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