4JNG

Schmallenberg virus nucleoprotein-RNA complex

Summary for 4JNG

• Entry DOI: 10.2210/pdb4jng/pdb
• Related: 4IDU 4IDX
• Descriptor: RNA (42-MER), Nucleocapsid protein (3 entities in total)
• Functional Keywords: negative-stranded rna virus nucleoprotein, bunyavirus, protect genomic rna, viral protein-rna complex, viral protein/rna
• Biological source: Schmallenberg virus (SBV)
• Cellular location: Virion: H2AM13
• Total number of polymer chains: 5
• Total formula weight: 117647.17

Authors

Dong, H.H.,Li, P.,Bottcher, B.,Elliott, R.M.,Dong, C.J. (deposition date: 2013-03-15, release date: 2013-07-31, Last modification date: 2023-11-08)

Primary citation

Dong, H.H.,Li, P.,Bottcher, B.,Elliott, R.M.,Dong, C.J.
Crystal structure of Schmallenberg orthobunyavirus nucleoprotein-RNA complex reveals a novel RNA sequestration mechanism.
Rna, 19:1129-1136, 2013

PubMed Abstract: Schmallenberg virus (SBV) is a newly emerged orthobunyavirus (family Bunyaviridae) that has caused severe disease in the offspring of farm animals across Europe. Like all orthobunyaviruses, SBV contains a tripartite negative-sense RNA genome that is encapsidated by the viral nucleocapsid (N) protein in the form of a ribonucleoprotein complex (RNP). We recently reported the three-dimensional structure of SBV N that revealed a novel fold. Here we report the crystal structure of the SBV N protein in complex with a 42-nt-long RNA to 2.16 Å resolution. The complex comprises a tetramer of N that encapsidates the RNA as a cross-shape inside the protein ring structure, with each protomer bound to 11 ribonucleotides. Eight bases are bound in the positively charged cleft between the N- and C-terminal domains of N, and three bases are shielded by the extended N-terminal arm. SBV N appears to sequester RNA using a different mechanism compared with the nucleoproteins of other negative-sense RNA viruses. Furthermore, the structure suggests that RNA binding results in conformational changes of some residues in the RNA-binding cleft and the N- and C-terminal arms. Our results provide new insights into the novel mechanism of RNA encapsidation by orthobunyaviruses.

PubMed: 23798666
DOI: 10.1261/rna.039057.113

Experimental method

X-RAY DIFFRACTION (2.12 Å)