Using Non-Crystallographic-Symmetry to solve the structure of a perfect merohedral twin crystal of Aichi virus (AiV)

C. Sabin & P. Plevka

Laboratory of Structural Virology, CEITEC, Masaryk University

Kamenice 5 / A35, Brno, 625 00, Czech Republic

charles.sabin@ceitec.muni.cz

Aichi virus (AiV) is associated with acute gastroenteritis and belongs to the family Picornaviridae of small (27-30nm in diameter), non-enveloped, positive-stranded RNA viruses [1-2]. The 2.3 Å resolution dataset collected from a cubic crystal of AiV particles displayed an apparent symmetry space group of I432 that truly revealed to be an I23 space group with a perfect merohedral twinning. A rotation-search using icosahedral 5-fold symmetry axes as probes in GLRF software [3] followed by a translation-search in the real space group have selected one of the possible twin orientations to position a capsid protein from Poliovirus as first template.

A twinning refinement method was used to determine the 'real' reflexion hkl contribution to the 'twinned' reflection 'hkl'. Thus for each reflexion, calculated twinned intensity Icalc('hkl'), twin operator (TWOP) and twin fraction (FRAC(hkl)) were defined such as:

 

Icalc('hkl') = 0.5 Icalc(hkl) + 0.5 Icalc(TWOP[hkl])

 

FRAC(hkl) = Icalc(hkl)/Icalc('hkl')

 

FRAC(hkl) was then applied to the observed intensity Iobs('hkl') as first approximation. Cycles of twinning refinement associated with real-space averaging of electron density map using Non-Crystallographic Symmetry were also required to manually build the model, improve phases and achieve the structure determination. The AiV capsid consists of a densely packed icosahedral arrangement of 60 protomers comprised of 3 polypeptides each.

 

1. Yamashita, T et al (1991) Isolation of cytopathic small round viruses with BS-C-1 cells from patients with gastroenteritis. J Infect Dis 164:954957.

2. Yamashita, T et al (1998) Complete nucleotide sequence and genetic organization of Aichi virus, a distinct member of the Picornaviridae associated with acute gastroenteritis in humans. J Virol 72:8408-8412

3. Tong,T. & Rossmann,M.G (1972) The Locked Rotation Function. Acta Cryst. A46:783-792.