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. 2006 Aug;80(16):7902-8.
doi: 10.1128/JVI.00483-06.

Dodecamer structure of severe acute respiratory syndrome coronavirus nonstructural protein nsp10

Dan Su  1 , Zhiyong Lou, Fei Sun, Yujia Zhai, Haitao Yang, Rongguang Zhang, Andrzej Joachimiak, Xuejun C Zhang, Mark Bartlam, Zihe Rao
Affiliations

Dodecamer structure of severe acute respiratory syndrome coronavirus nonstructural protein nsp10

Dan Su et al. J Virol. 2006 Aug.

Abstract

The severe acute respiratory syndrome coronavirus (SARS-CoV) nonstructural proteins nsp1 to nsp16 have been implicated by genetic analysis in the assembly of a functional replication/transcription complex. We report the crystal structure of nsp10 from SARS-CoV at 2.1-A resolution. The nsp10 structure has a novel fold, and 12 identical subunits assemble to form a unique spherical dodecameric architecture. Two zinc fingers have been identified from the nsp10 monomer structure with the sequence motifs C-(X)2-C-(X)5-H-(X)6-C and C-(X)2-C-(X)7-C-(X)-C. The nsp10 crystal structure is the first of a new class of zinc finger protein three-dimensional structures to be revealed experimentally. The zinc finger sequence motifs are conserved among all three coronavirus antigenic groups, implicating an essential function for nsp10 in all coronaviruses. Based on the structure, we propose that nsp10 is a transcription factor for coronavirus replication/transcription.

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Figures

FIG. 1.
FIG. 1.
Ribbon representation of the nsp10 crystal structure. A. One nsp10 trimer is viewed along the noncrystallography threefold axis from the outside of a dodecamer. The three protomers are colored in magenta, gold, and green. B. The remaining three trimers of the dodecamer are shown in the same orientation as that for panel A using the same color scheme. C. The same as panel B but rotated by 90°. D. The relationship between threefold axes. The twist angle between pairs of threefold axes is approximately 108°. E. The complete dodecamer structure of SARS-CoV nsp10. The three protomers in a trimer are colored in magenta, gold, and green. This figure was prepared with the programs Molscript (8), Bobscript (5), and Raster3D (10).
FIG. 2.
FIG. 2.
Electrostatic potential of the nsp10 crystal structure. A. The electrostatic potential of a complete dodecamer is mapped on its outer molecular surface. Negatively charged regions are colored in red, positively charged regions are colored in blue, and neutral regions are colored in gray. The C-terminal-bound zinc ions, which are located on the outer surface, are depicted as red spheres. The position of the front trimer is highlighted by a triangle. B. The inner surface electrostatic potential of the dodecamer is shown in the same orientation as that of panel A. C. A cross-section of the nsp10 dodecamer to illustrate the minimum and maximum radii of the shell. D. The electrostatic potential surface of an isolated trimer. This figure was drawn with the program CCP4 mg (12, 13).
FIG. 3.
FIG. 3.
nsp10 monomer fold. A. Stereo diagram showing a Cα trace of the nsp10 monomer. Two zinc ions are shown as gray spheres, and one chelating water molecule is shown as a smaller red sphere. B. Stereo ribbon diagram of the nsp10 monomer with β-strands in purple and α-helices in gold. Secondary structure elements are labeled. This view is rotated by ∼90° relative to that of panel A. This figure was prepared with the programs Molscript (8), Bobscript (5), and Raster3D (10).
FIG. 4.
FIG. 4.
Stereo views of the two independent zinc binding sites. A. The N-terminal zinc binding site with electron density. Key residues interacting with the zinc ion are labeled and depicted as sticks with carbon, nitrogen, oxygen, and sulfur atoms colored in yellow, blue, red, and green, respectively. The zinc ion is shown as a gray sphere. A refined-model-phased 2Fo-Fc electron density map is shown for the zinc ion and chelated residues at 1.3 σ. Secondary structure elements are labeled. B. The C-terminal zinc binding site with electron density. The turn between C117 and C120 is labeled. This figure was prepared with the programs Molscript (8), Bobscript (5), and Raster3D (10).
FIG. 5.
FIG. 5.
Multiple-sequence alignment of SARS-CoV nsp10 with representatives from all three groups of the genus Coronavirus. HCOV-229E, human coronavirus strain 229E; MHV, mouse hepatitis virus; IBV, avian infectious bronchiolitis virus. The secondary structure for SARS-CoV is shown at the top of the alignment; arrows indicate β-strands, and helical curves denote α- or 310-helices. Residues highlighted in red are identical among the compared proteins; residues highlighted in yellow are conserved. Residues important for zinc binding are marked with green triangles, and residues important for stability of the dodecamer are marked with blue vertical arrows. The alignment was generated by ClustalX (20) and drawn with ESPript (6).
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