+データを開く
-基本情報
登録情報 | データベース: PDB / ID: 3c6d | ||||||
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タイトル | The pseudo-atomic structure of dengue immature virus | ||||||
要素 |
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キーワード | VIRUS / icosahedral virion / Helicase / Hydrolase / Nucleotide-binding / RNA replication / Transmembrane / ATP-binding / Capsid protein / Cleavage on pair of basic residues / Endoplasmic reticulum / Envelope protein / Glycoprotein / Metal-binding / Multifunctional enzyme / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / Ribonucleoprotein / RNA-binding / RNA-directed RNA polymerase / Secreted / Serine protease / Transcription / Transcription regulation / Transferase / Viral nucleoprotein / 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 / protein complex oligomerization / ribonucleoside triphosphate phosphatase activity / monoatomic ion channel activity / channel activity / double-stranded RNA binding ...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 / protein complex oligomerization / ribonucleoside triphosphate phosphatase activity / monoatomic ion channel activity / channel activity / double-stranded RNA binding / nucleoside-triphosphate phosphatase / viral capsid / monoatomic ion transmembrane transport / 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 / protein dimerization activity / host cell endoplasmic reticulum membrane / RNA helicase / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / 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 / 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 Thailand/16681/84 (デング熱ウイルス) Dengue virus 2 (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: 12.5 Å | ||||||
データ登録者 | Li, L. | ||||||
引用 | ジャーナル: Science / 年: 2008 タイトル: The flavivirus precursor membrane-envelope protein complex: structure and maturation. 著者: Long Li / Shee-Mei Lok / I-Mei Yu / Ying Zhang / Richard J Kuhn / Jue Chen / Michael G Rossmann / 要旨: Many viruses go through a maturation step in the final stages of assembly before being transmitted to another host. The maturation process of flaviviruses is directed by the proteolytic cleavage of ...Many viruses go through a maturation step in the final stages of assembly before being transmitted to another host. The maturation process of flaviviruses is directed by the proteolytic cleavage of the precursor membrane protein (prM), turning inert virus into infectious particles. We have determined the 2.2 angstrom resolution crystal structure of a recombinant protein in which the dengue virus prM is linked to the envelope glycoprotein E. The structure represents the prM-E heterodimer and fits well into the cryo-electron microscopy density of immature virus at neutral pH. The pr peptide beta-barrel structure covers the fusion loop in E, preventing fusion with host cell membranes. The structure provides a basis for identifying the stages of its pH-directed conformational metamorphosis during maturation, ending with release of pr when budding from the host. | ||||||
履歴 |
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-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 | 3c6d.cif.gz | 56.8 KB | 表示 | PDBx/mmCIF形式 |
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PDB形式 | pdb3c6d.ent.gz | 35.5 KB | 表示 | PDB形式 |
PDBx/mmJSON形式 | 3c6d.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 | 3c6d_validation.pdf.gz | 776.9 KB | 表示 | wwPDB検証レポート |
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文書・詳細版 | 3c6d_full_validation.pdf.gz | 776.5 KB | 表示 | |
XML形式データ | 3c6d_validation.xml.gz | 21.6 KB | 表示 | |
CIF形式データ | 3c6d_validation.cif.gz | 32.5 KB | 表示 | |
アーカイブディレクトリ | https://data.pdbj.org/pub/pdb/validation_reports/c6/3c6d ftp://data.pdbj.org/pub/pdb/validation_reports/c6/3c6d | 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: (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: 43904.410 Da / 分子数: 3 / 由来タイプ: 天然 由来: (天然) Dengue virus 2 Thailand/16681/84 (デング熱ウイルス) 属: Flavivirus / 生物種: Dengue virus / 株: 16681 / 参照: UniProt: O11875, UniProt: A7TUD3*PLUS #2: タンパク質 | 分子量: 9261.531 Da / 分子数: 3 / 由来タイプ: 天然 / 由来: (天然) Dengue virus 2 (デング熱ウイルス) / 属: Flavivirus / 生物種: Dengue virus / 株: 2 / 参照: UniProt: P14337, UniProt: Q3BCY5*PLUS 配列の詳細 | THE AUTHOR STATES THAT THE DIFFERENCES BETWEEN THE SEQUENCE AND THE SEQUENCE IN THE DATABASE ...THE AUTHOR STATES THAT THE DIFFERENCE | |
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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-2 IMMATURE PARTICLE / タイプ: VIRUS 詳細: THE SAMPLES WERE PRODUCED BY ADDING AMMONIUM CHLORIDE TO THE MEDIA IN THE LATE INFECTION STAGE |
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ウイルスについての詳細 | ホストのカテゴリ: VERTEBRATES / 単離: STRAIN / タイプ: VIRION |
天然宿主 | 生物種: Aedes aegypti / 株: C6/36 |
緩衝液 | pH: 7.6 / 詳細: 12 mM Tris-HCl, 120 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 | 装置: HOMEMADE PLUNGER / 凍結剤: ETHANE |
-電子顕微鏡撮影
顕微鏡 | モデル: FEI/PHILIPS CM300FEG/T / 日付: 2008年4月4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 FIELD / 倍率(公称値): 45000 X / 倍率(補正後): 33000 X / 最大 デフォーカス(公称値): 3640 nm / 最小 デフォーカス(公称値): 1662 nm / Cs: 2 mm |
試料ホルダ | 温度: 100 K / 傾斜角・最大: 0 ° / 傾斜角・最小: 0 ° |
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 | 解像度: 12.5 Å / 粒子像の数: 2741 / 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: USE PROGRAM EMFIT, SEARCH FOR POSTION WHERE ATOMS OCCUPY MOST EM DENSITY PEAKS 詳細: METHOD--SEE PRIMARY CITATION REFINEMENT PROTOCOL--RIGID BODY | |||||||||||||||||||||
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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