1ZDH

MS2 COAT PROTEIN/RNA COMPLEX

Summary for 1ZDH

• Entry DOI: 10.2210/pdb1zdh/pdb
• Descriptor: RNA (5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*CP*AP*U P*GP*U)-3'), PROTEIN (BACTERIOPHAGE MS2 COAT PROTEIN) (3 entities in total)
• Functional Keywords: complex (coat protein-rna), coat protein, rna-binding, viral protein capsid, rna fragment, icosahedral virus, virus-rna complex, virus/rna
• Biological source: Enterobacterio phage MS2; More
• Cellular location: Virion : P03612
• Total number of polymer chains: 5
• Total formula weight: 53338.74

Authors

Valegard, K.,Van Den Worm, S.,Liljas, L. (deposition date: 1996-09-24, release date: 1997-04-21, Last modification date: 2023-04-19)

Primary citation

Valegard, K.,Murray, J.B.,Stonehouse, N.J.,van den Worm, S.,Stockley, P.G.,Liljas, L.
The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions.
J.Mol.Biol., 270:724-738, 1997

PubMed Abstract: Crystal structures of two complexes between recombinant MS2 capsids and RNA operator fragments have been determined at 2.7 A resolution. The coat protein of the RNA bacteriophage MS2 is bifunctional; it forms the icosahedral virus shell to protect the viral nucleic acid and it acts as a translational repressor by binding with high specificity to a unique site on the RNA, a single stem-loop structure, containing the initiation codon of the gene for the viral replicase. In order to determine the structure of these protein-RNA complexes, we have used chemically synthesized variants of the stem-loop fragment and soaked them into crystals of recombinant capsids. The RNA stem-loop, as bound to the protein, forms a crescent-like structure and interacts with the surface of the beta-sheet of a coat protein dimer. It makes protein contacts with seven phosphate groups on the 5' side of the stem-loop, with a pyrimidine base at position -5, which stacks onto a tyrosine, and with two exposed adenine bases, one in the loop and one at a bulge in the stem. Replacement of the wild-type uridine with a cytosine at position -5 increases the affinity of the RNA to the dimer significantly. The complex with RNA stem-loop having cytosine at this position differs from that of the wild-type complex mainly by having one extra intramolecular RNA interaction and one extra water-mediated hydrogen bond.

PubMed: 9245600
DOI: 10.1006/jmbi.1997.1144

Experimental method

X-RAY DIFFRACTION (2.7 Å)