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データを開く
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基本情報
登録情報 | データベース: PDB / ID: 7qrf | ||||||||||||
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タイトル | Structure of the dimeric complex between precursor membrane ectodomain (prM) and envelope protein ectodomain (E) from tick-borne encephalitis virus | ||||||||||||
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![]() | VIRAL PROTEIN / class II fusion envelope protein / precursor membrane protein / chaperone / flavivirus maturation / trans-golgi acid pH | ||||||||||||
機能・相同性 | ![]() 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 / viral capsid / 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 / double-stranded RNA binding / viral capsid / 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 type I interferon-mediated signaling pathway / RNA helicase / 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 / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding 類似検索 - 分子機能 | ||||||||||||
生物種 | ![]() | ||||||||||||
手法 | ![]() ![]() ![]() | ||||||||||||
![]() | Vaney, M.C. / Rouvinski, A. / Rey, F.A. | ||||||||||||
資金援助 | ![]()
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![]() | ![]() タイトル: Evolution and activation mechanism of the flavivirus class II membrane-fusion machinery. 著者: Vaney, M.C. / Dellarole, M. / Duquerroy, S. / Medits, I. / Tsouchnikas, G. / Rouvinski, A. / England, P. / Stiasny, K. / Heinz, F.X. / Rey, F.A. #1: ![]() 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. | ||||||||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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ダウンロードとリンク
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ダウンロード
PDBx/mmCIF形式 | ![]() | 205.5 KB | 表示 | ![]() |
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PDB形式 | ![]() | 161.1 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
文書・要旨 | ![]() | 700.3 KB | 表示 | ![]() |
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文書・詳細版 | ![]() | 703.7 KB | 表示 | |
XML形式データ | ![]() | 18.9 KB | 表示 | |
CIF形式データ | ![]() | 25.9 KB | 表示 | |
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
-関連構造データ
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リンク
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集合体
登録構造単位 | ![]()
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1 | ![]()
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単位格子 |
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Components on special symmetry positions |
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要素
-タンパク質 , 2種, 2分子 AD
#1: タンパク質 | 分子量: 47867.855 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: The N-terminal end of E (Molecule 1) is linked to the C-terminal of ectodomain prM (Molecule 3) by a linker of 14 residues (GGGGENLYFQGGGG). This linker of 14 residues is only described in ...詳細: The N-terminal end of E (Molecule 1) is linked to the C-terminal of ectodomain prM (Molecule 3) by a linker of 14 residues (GGGGENLYFQGGGG). This linker of 14 residues is only described in the sequence of E (Molecule 1) at its N-terminal. For purification, at the C-terminal of E it is added an enterokinase site with a dstrep-tag sequence : (GPFEDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK). 由来: (組換発現) ![]() 株: Neudoerfl / プラスミド: PT389 / Cell (発現宿主): SCHNEIDER 2 発現宿主: ![]() ![]() 参照: UniProt: P14336 |
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#3: タンパク質 | 分子量: 15290.941 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: The C-terminal end of prM (Molecule 3) is linked to the N-terminal of E (Molecule 1) by a linker of 14 residues (GGGGENLYFQGGGG). This linker is described in the sequence of E (Molecule 1). ...詳細: The C-terminal end of prM (Molecule 3) is linked to the N-terminal of E (Molecule 1) by a linker of 14 residues (GGGGENLYFQGGGG). This linker is described in the sequence of E (Molecule 1). The furin site is deleted from one amino acid (Arginine). Intact furin site : ...RTRRSVL... Mutated furin site : ...RTRSVL... 由来: (組換発現) ![]() 株: Neudoerfl / プラスミド: PT389 / Cell (発現宿主): SCHNEIDER 2 発現宿主: ![]() ![]() 参照: UniProt: P14336 |
-タンパク質・ペプチド , 1種, 1分子 C
#2: タンパク質・ペプチド | 分子量: 443.539 Da / 分子数: 1 / 由来タイプ: 組換発現 詳細: This peptide should be part of the M ectodomain but we were unable to attribute the true sequence. 由来: (組換発現) ![]() 株: NEUDOERFL / プラスミド: PT389 / Cell (発現宿主): SCHNEIDER 2 発現宿主: ![]() ![]() |
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-非ポリマー , 4種, 84分子 ![](data/chem/img/SO4.gif)
![](data/chem/img/PE4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PE4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/HOH.gif)
#4: 化合物 | ChemComp-SO4 / | ||
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#5: 化合物 | ChemComp-PE4 / | ||
#6: 化合物 | ChemComp-EDO / #7: 水 | ChemComp-HOH / | |
-詳細
研究の焦点であるリガンドがあるか | N |
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-実験情報
-実験
実験 | 手法: ![]() |
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試料調製
結晶 | マシュー密度: 2.97 Å3/Da / 溶媒含有率: 58.63 % |
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結晶化 | 温度: 293 K / 手法: 蒸気拡散法 / pH: 3.5 詳細: 0.2M Li(SO4), 0.1M Na citrate pH 3.5, 28% (v/v) PEG 400 |
-データ収集
回折 | 平均測定温度: 100 K / Serial crystal experiment: N |
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放射光源 | 由来: ![]() ![]() ![]() |
検出器 | タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2014年2月14日 |
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 | 波長: 0.97934 Å / 相対比: 1 |
反射 | 解像度: 2.28→49 Å / Num. obs: 28985 / % possible obs: 95 % / 冗長度: 19.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.023 / Rrim(I) all: 0.099 / Net I/σ(I): 19.8 |
反射 シェル | 解像度: 2.28→2.435 Å / Rmerge(I) obs: 2.623 / Num. unique obs: 1449 / CC1/2: 0.323 / Rpim(I) all: 0.891 / Rrim(I) all: 2.699 |
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解析
ソフトウェア |
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精密化 | 構造決定の手法: ![]() 開始モデル: 1SVB, 3C5X 解像度: 2.28→28.42 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.222 / 交差検証法: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.217 / SU Rfree Blow DPI: 0.18 / SU Rfree Cruickshank DPI: 0.183 詳細: The BUSTER refinement was done against the STARANISO corrected intensity from anisotropy. This is the reason why, in the last shell of resolution, the completness is 7% while the working ...詳細: The BUSTER refinement was done against the STARANISO corrected intensity from anisotropy. This is the reason why, in the last shell of resolution, the completness is 7% while the working Rfactor is higher than the free Rfactor. All the refinement stastitics introduced here are from the STARANISO statistics output.
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原子変位パラメータ | Biso max: 178.25 Å2 / Biso mean: 80.83 Å2 / Biso min: 44.08 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化ステップ | サイクル: final / 解像度: 2.28→28.42 Å
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拘束条件 |
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LS精密化 シェル | 解像度: 2.28→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 15
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精密化 TLS | 手法: refined / Refine-ID: X-RAY DIFFRACTION
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精密化 TLSグループ |
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