ジャーナル: Structure / 年: 2013 タイトル: Plate tectonics of virus shell assembly and reorganization in phage φ8, a distant relative of mammalian reoviruses. 著者: Kamel El Omari / Geoff Sutton / Janne J Ravantti / Hanwen Zhang / Thomas S Walter / Jonathan M Grimes / Dennis H Bamford / David I Stuart / Erika J Mancini / 要旨: The hallmark of a virus is its capsid, which harbors the viral genome and is formed from protein subunits, which assemble following precise geometric rules. dsRNA viruses use an unusual protein ...The hallmark of a virus is its capsid, which harbors the viral genome and is formed from protein subunits, which assemble following precise geometric rules. dsRNA viruses use an unusual protein multiplicity (120 copies) to form their closed capsids. We have determined the atomic structure of the capsid protein (P1) from the dsRNA cystovirus Φ8. In the crystal P1 forms pentamers, very similar in shape to facets of empty procapsids, suggesting an unexpected assembly pathway that proceeds via a pentameric intermediate. Unlike the elongated proteins used by dsRNA mammalian reoviruses, P1 has a compact trapezoid-like shape and a distinct arrangement in the shell, with two near-identical conformers in nonequivalent structural environments. Nevertheless, structural similarity with the analogous protein from the mammalian viruses suggests a common ancestor. The unusual shape of the molecule may facilitate dramatic capsid expansion during phage maturation, allowing P1 to switch interaction interfaces to provide capsid plasticity.
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: 0.9326 Å / 相対比: 1
反射
解像度: 3.7→30 Å / Num. obs: 271956 / % possible obs: 97.1 % / Observed criterion σ(I): 2.1 / 冗長度: 11.1 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 15.1
反射 シェル
解像度: 3.7→3.83 Å / 冗長度: 4.8 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 2.1 / % possible all: 71.3
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解析
ソフトウェア
名称
バージョン
分類
REFMAC
5.7.0032
精密化
HKL-2000
データ削減
SCALEPACK
データスケーリング
HKL2Map
位相決定
精密化
構造決定の手法: 単波長異常分散 開始モデル: NONE 解像度: 3.7→30.01 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.919 / SU B: 28.249 / SU ML: 0.387 / 交差検証法: THROUGHOUT / ESU R: 1.372 / ESU R Free: 0.465 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD 詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
Rfactor
反射数
%反射
Selection details
Rfree
0.25836
13628
5 %
RANDOM
Rwork
0.24448
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-
-
obs
0.24519
256979
96.96 %
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溶媒の処理
イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK