4J1G

Leanyer orthobunyavirus nucleoprotein-ssRNA complex

Summary for 4J1G

• Entry DOI: 10.2210/pdb4j1g/pdb
• Related: 4J1J
• Descriptor: Nucleocapsid, RNA (45-MER) (3 entities in total)
• Functional Keywords: protein-rna complex, rna binding protein, rna binding, nucleocapsid protein, viral protein-rna complex, viral protein/rna
• Biological source: Leanyer virus
• Total number of polymer chains: 5
• Total formula weight: 118913.50

Authors

Niu, F.,Shaw, N.,Wang, Y.,Jiao, L.,Ding, W.,Li, X.,Zhu, P.,Upur, H.,Ouyang, S.,Cheng, G.,Liu, Z.J. (deposition date: 2013-02-01, release date: 2013-04-10, Last modification date: 2024-02-28)

Primary citation

Niu, F.,Shaw, N.,Wang, Y.E.,Jiao, L.,Ding, W.,Li, X.,Zhu, P.,Upur, H.,Ouyang, S.,Cheng, G.,Liu, Z.J.
Structure of the Leanyer orthobunyavirus nucleoprotein-RNA complex reveals unique architecture for RNA encapsidation.
Proc.Natl.Acad.Sci.USA, 110:9054-9059, 2013

PubMed Abstract: Negative-stranded RNA viruses cover their genome with nucleoprotein (N) to protect it from the human innate immune system. Abrogation of the function of N offers a unique opportunity to combat the spread of the viruses. Here, we describe a unique fold of N from Leanyer virus (LEAV, Orthobunyavirus genus, Bunyaviridae family) in complex with single-stranded RNA refined to 2.78 Å resolution as well as a 2.68 Å resolution structure of LEAV N-ssDNA complex. LEAV N is made up of an N- and a C-terminal lobe, with the RNA binding site located at the junction of these lobes. The LEAV N tetramer binds a 44-nucleotide-long single-stranded RNA chain. Hence, oligomerization of N is essential for encapsidation of the entire genome and is accomplished by using extensions at the N and C terminus. Molecular details of the oligomerization of N are illustrated in the structure where a circular ring-like tertiary assembly of a tetramer of LEAV N is observed tethering the RNA in a positively charged cavity running along the inner edge. Hydrogen bonds between N and the C2 hydroxyl group of ribose sugar explain the specificity of LEAV N for RNA over DNA. In addition, base-specific hydrogen bonds suggest that some regions of RNA bind N more tightly than others. Hinge movements around F20 and V125 assist in the reversal of capsidation during transcription and replication of the virus. Electron microscopic images of the ribonucleoprotein complexes of LEAV N reveal a filamentous assembly similar to those found in phleboviruses.

PubMed: 23569220
DOI: 10.1073/pnas.1300035110

Experimental method

X-RAY DIFFRACTION (2.789 Å)