5BKN

Crystallographic structure of a cubic crystal form of STMV (84.5 degree rotation) grown from chloride

This is a non-PDB format compatible entry.

Summary for 5BKN

• Entry DOI: 10.2210/pdb5bkn/pdb
• Descriptor: Coat protein, RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*U)-3'), RNA (5'-R(P*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3'), ... (14 entities in total)
• Functional Keywords: anions, rna, ion channel, fivefold vertex, crystallization, virus
• Biological source: Satellite tobacco mosaic virus (STMV); More
• Total number of polymer chains: 39
• Total formula weight: 404925.49

Authors

McPherson, A. (deposition date: 2021-03-20, release date: 2021-12-15, Last modification date: 2023-09-27)

Primary citation

McPherson, A.
Structures of additional crystal forms of Satellite tobacco mosaic virus grown from a variety of salts.
Acta Crystallogr.,Sect.F, 77:473-483, 2021

PubMed Abstract: The structures of new crystal forms of Satellite tobacco mosaic virus (STMV) are described. These belong to space groups I2, P222 (a low-resolution form), R3 (H3) and P23. The R3 crystals are 50%/50% twinned, as are two instances of the P23 crystals. The I2 and P222 crystals were grown from ammonium sulfate solutions, as was one crystal in space group P23, while the R3 and the other P23 crystals were grown from sodium chloride, sodium bromide and sodium nitrate. The monoclinic and orthorhombic crystals have half a virus particle as the asymmetric unit, while the rhombohedral and cubic crystals have one third of a virus particle. RNA segments organized about the icosahedral twofold axes were present in crystals grown from ammonium sulfate and sodium chloride, as in the canonical I222 crystals (PDB entry 4oq8), but were not observed in crystals grown from sodium bromide and sodium nitrate. Bromide and nitrate ions generally replaced the RNA phosphates present in the I222 crystals, including the phosphates seen on fivefold axes, and were also found at threefold vertices in both the rhombohedral and cubic forms. An additional anion was also found on the fivefold axis 5 Å from the first anion, and slightly outside the capsid in crystals grown from sodium chloride, sodium bromide and sodium nitrate, suggesting that the path along the symmetry axis might be an ion channel. The electron densities for RNA strands at individual icosahedral dyads, as well as at the amino-terminal peptides of protein subunits, exhibited a diversity of orientations, in particular the residues at the ends.

PubMed: 34866603
DOI: 10.1107/S2053230X21011547

Experimental method

X-RAY DIFFRACTION (3 Å)