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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: 1ev1 | ||||||
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タイトル | ECHOVIRUS 1 | ||||||
![]() | (ECHOVIRUS 1) x 4 | ||||||
![]() | VIRUS / VIRAL COAT PROTEIN / CAPSID / PICORNAVIRUS / ECHOVIRUS / Icosahedral virus | ||||||
機能・相同性 | ![]() caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity ...caveolin-mediated endocytosis of virus by host cell / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / DNA replication / RNA helicase activity / symbiont-mediated activation of host autophagy / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / virion attachment to host cell / host cell nucleus / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane 類似検索 - 分子機能 | ||||||
生物種 | ![]() | ||||||
手法 | ![]() ![]() | ||||||
![]() | Wien, M.W. / Filman, D.J. / Hogle, J.M. | ||||||
![]() | ![]() タイトル: Structure determination of echovirus 1. 著者: D J Filman / M W Wien / J A Cunningham / J M Bergelson / J M Hogle / ![]() 要旨: The atomic structure of echovirus 1 (a member of the enterovirus genus of the picornavirus family) has been determined using cryo-crystallography and refined to 3.55 A resolution. Echovirus 1 ...The atomic structure of echovirus 1 (a member of the enterovirus genus of the picornavirus family) has been determined using cryo-crystallography and refined to 3.55 A resolution. Echovirus 1 crystallizes in space group P22121 with a = 352.45, b = 472.15 and c = 483.20 A. The crystals contain one full virus particle in the asymmetric unit allowing for 60-fold noncrystallographic symmetry averaging. The diffraction pattern shows strong pseudo-B-centering with reflections with h + l = 2n + 1 being systematically weak or absent below about 6 A resolution. The size of the unit cell and presence of pseudo-B-centering placed strong constraints on the allowed packing of the icosahedral particle in the crystal lattice. These constraints greatly facilitated the determination of the orientation and position of the virus by reducing the dimensionality of the search, but interactions between the crystallographic and noncrystallographic symmetries rendered the choice of space group ambiguous until very late in the structure determination. This structure determination provides a striking example of the power of packing analysis in molecular replacement and illustrates how subtle interactions between crystallographic and noncrystallographic symmetries can be resolved. #1: ![]() タイトル: A Pseudo-Cell Based Approach to Efficient Crystallographic Refinement of Viruses 著者: Jacobson, D.H. / Hogle, J.M. / Filman, D.J. | ||||||
履歴 |
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構造の表示
構造ビューア | 分子: ![]() ![]() |
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PDBx/mmCIF形式 | ![]() | 158.1 KB | 表示 | ![]() |
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PDB形式 | ![]() | 119.6 KB | 表示 | ![]() |
PDBx/mmJSON形式 | ![]() | ツリー表示 | ![]() | |
その他 | ![]() |
-検証レポート
アーカイブディレクトリ | ![]() ![]() | HTTPS FTP |
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-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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単位格子 |
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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)) |
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要素
-タンパク質 , 4種, 4分子 1234
#1: タンパク質 | 分子量: 31604.373 Da / 分子数: 1 / 断片: VP1, VP2, VP3, VP4 / 由来タイプ: 天然 詳細: ECHOVIRUS OBTAINED FROM THE ATCC, PASSED IN HELA CELLS, THEN PLAQUE PURIFIED AND EXPANDED 由来: (天然) ![]() |
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#2: タンパク質 | 分子量: 28126.465 Da / 分子数: 1 / 断片: VP1, VP2, VP3, VP4 / 由来タイプ: 天然 詳細: ECHOVIRUS OBTAINED FROM THE ATCC, PASSED IN HELA CELLS, THEN PLAQUE PURIFIED AND EXPANDED 由来: (天然) ![]() |
#3: タンパク質 | 分子量: 26471.074 Da / 分子数: 1 / 断片: VP1, VP2, VP3, VP4 / 由来タイプ: 天然 詳細: ECHOVIRUS OBTAINED FROM THE ATCC, PASSED IN HELA CELLS, THEN PLAQUE PURIFIED AND EXPANDED 由来: (天然) ![]() |
#4: タンパク質 | 分子量: 7398.131 Da / 分子数: 1 / 断片: VP1, VP2, VP3, VP4 / 由来タイプ: 天然 詳細: ECHOVIRUS OBTAINED FROM THE ATCC, PASSED IN HELA CELLS, THEN PLAQUE PURIFIED AND EXPANDED 由来: (天然) ![]() |
-非ポリマー , 3種, 16分子 1





#5: 化合物 | #6: 化合物 | ChemComp-MYR / | #7: 水 | ChemComp-HOH / | |
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-詳細
Has protein modification | Y |
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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: 2.59 Å3/Da / 溶媒含有率: 30 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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結晶化 | pH: 7 / 詳細: pH 7.0 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
結晶化 | *PLUS 温度: 277 K / pH: 6 / 手法: microdialysis | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶液の組成 | *PLUS
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-データ収集
回折 | 平均測定温度: 113 K |
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放射光源 | 由来: ![]() |
検出器 | タイプ: MARRESEARCH / 検出器: AREA DETECTOR / 日付: 1996年8月1日 / 詳細: SUPPER LONG MIRRORS |
放射 | モノクロメーター: SUPPER LONG MIRRORS / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray |
放射波長 | 波長: 1.5418 Å / 相対比: 1 |
反射 | 解像度: 3.55→50 Å / Num. obs: 947283 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / 冗長度: 3.7 % / Rmerge(I) obs: 0.136 |
反射 シェル | 解像度: 3.55→3.66 Å / Rmerge(I) obs: 0.241 |
反射 | *PLUS Num. measured all: 3522138 |
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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: ![]() Isotropic thermal model: ISOTROPIC THERMAL MOTION THE MODEL WAS TAKEN INTO ACCOUNT BY USING 12 OR 16 RESOLUTION-DEPENDENT BIN SCALES IN ALL STRUCTURE FACTOR COMPARISONS. 詳細: PROTOMER-BOX-BASED PSEUDO-REAL-SPACE PROGRAM BY FILMAN, JACOBSON, AND HOGLE WAS ALSO USED.
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精密化ステップ | サイクル: LAST / 解像度: 3.55→50 Å
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拘束条件 |
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Refine LS restraints NCS | NCS model details: STRICT ICOSAHEDRAL SYMMETRY WAS ENFORCED. TO GENERATE THE ASYMMETRIC UNIT IN P 21 21 2, THE ICOSAHEDRAL PARTICLE WAS ROTATED BY THE MATRIX: 0.52131 0.85335 -.00519 -.00061 0.00646 ...NCS model details: STRICT ICOSAHEDRAL SYMMETRY WAS ENFORCED. TO GENERATE THE ASYMMETRIC UNIT IN P 21 21 2, THE ICOSAHEDRAL PARTICLE WAS ROTATED BY THE MATRIX: 0.52131 0.85335 -.00519 -.00061 0.00646 0.99998 0.85337 -.52129 0.00389 AND TRANSLATED TO THE FRACTIONAL COORDINATES: 0.24950 0.19623 0.25000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS精密化 シェル | 解像度: 3.55→3.66 Å / Total num. of bins used: 16 /
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ソフトウェア | *PLUS 名称: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
精密化 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
溶媒の処理 | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
原子変位パラメータ | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
拘束条件 | *PLUS
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LS精密化 シェル | *PLUS Rfactor obs: 0.298 |