7lyf

From Proteopedia

Dengue virus RNA promoter stem-loop A fused with tRNA-scaffold

Structural highlights

7lyf is a 1 chain structure with sequence from Dengue virus 2. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.4Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Flaviviruses use a ~70 nucleotide stem-loop structure called stem-loop A (SLA) at the 5' end of the RNA genome as a promoter for RNA synthesis. Flaviviral polymerase NS5 specifically recognizes SLA to initiate RNA synthesis and methylate the 5' guanosine cap. We report the crystal structures of dengue (DENV) and Zika virus (ZIKV) SLAs. DENV and ZIKV SLAs differ in the relative orientations of their top stem-loop helices to bottom stems, but both form an intermolecular three-way junction with a neighboring SLA molecule. To understand how NS5 engages SLA, we determined the SLA-binding site on NS5 and modeled the NS5-SLA complex of DENV and ZIKV. Our results show that the gross conformational differences seen in DENV and ZIKV SLAs can be compensated by the differences in the domain arrangements in DENV and ZIKV NS5s. We describe two binding modes of SLA and NS5 and propose an SLA-mediated RNA synthesis mechanism.

Structures of flavivirus RNA promoters suggest two binding modes with NS5 polymerase.,Lee E, Bujalowski PJ, Teramoto T, Gottipati K, Scott SD, Padmanabhan R, Choi KH Nat Commun. 2021 May 5;12(1):2530. doi: 10.1038/s41467-021-22846-1. PMID:33953197^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Lee E, Bujalowski PJ, Teramoto T, Gottipati K, Scott SD, Padmanabhan R, Choi KH. Structures of flavivirus RNA promoters suggest two binding modes with NS5 polymerase. Nat Commun. 2021 May 5;12(1):2530. doi: 10.1038/s41467-021-22846-1. PMID:33953197 doi:http://dx.doi.org/10.1038/s41467-021-22846-1