4H5O

Crystal Structure of Rift Valley Fever Virus Nucleocapsid Protein Pentamer Bound to Single-stranded RNA

Summary for 4H5O

• Entry DOI: 10.2210/pdb4h5o/pdb
• Related: 4H5L 4H5M 4H5P 4H5Q 4H6F 4H6G
• Descriptor: Nucleocapsid protein, 35-mer poly(U) RNA (2 entities in total)
• Functional Keywords: nucleocapsid protein, n protein, ribonucleoprotein, viral nucleoprotein, rna binding, virus, rnp, viral protein-rna complex, viral protein/rna
• Biological source: Rift Valley fever virus (RVFV)
• Total number of polymer chains: 12
• Total formula weight: 295007.16

Authors

Raymond, D.D.,Smith, J.L. (deposition date: 2012-09-18, release date: 2012-11-07, Last modification date: 2023-09-20)

Primary citation

Raymond, D.D.,Piper, M.E.,Gerrard, S.R.,Skiniotis, G.,Smith, J.L.
Phleboviruses encapsidate their genomes by sequestering RNA bases.
Proc.Natl.Acad.Sci.USA, 109:19208-19213, 2012

PubMed Abstract: Rift Valley fever and Toscana viruses are human pathogens for which no effective therapeutics exist. These and other phleboviruses have segmented negative-sense RNA genomes that are sequestered by a nucleocapsid protein (N) to form ribonucleoprotein (RNP) complexes of irregular, asymmetric structure, previously uncharacterized at high resolution. N binds nonspecifically to single-stranded RNA with nanomolar affinity. Crystal structures of Rift Valley fever virus N-RNA complexes reconstituted with defined RNAs of different length capture tetrameric, pentameric and hexameric N-RNA multimers. All N-N subunit contacts are mediated by a highly flexible α-helical arm. Arm movement gives rise to the three multimers in the crystal structures and also explains the asymmetric architecture of the RNP. Despite the flexible association of subunits, the crystal structures reveal an invariant, monomeric RNP building block, consisting of the core of one N subunit, the arm of a neighboring N, and four RNA nucleotides with the flanking phosphates. Up to three additional RNA nucleotides bind between subunits. The monomeric building block is matched in size to the repeating unit in viral RNP, as visualized by electron microscopy. N sequesters four RNA bases in a narrow hydrophobic binding slot and has polar contacts only with the sugar-phosphate backbone, which faces the solvent. All RNA bases, whether in the binding slot or in the subunit interface, face the protein in a manner that is incompatible with base pairing or with "reading" by the viral polymerase.

PubMed: 23129612
DOI: 10.1073/pnas.1213553109

Experimental method

X-RAY DIFFRACTION (3.9 Å)