6MWN

Crystal structure of hepatitis A virus IRES domain V in complex with Fab HAVx

Summary for 6MWN

• Entry DOI: 10.2210/pdb6mwn/pdb
• Descriptor: HAV dV RNA (92-MER), Fab HAVx Heavy Chain, Fab HAVx Light Chain, ... (4 entities in total)
• Functional Keywords: rna, chaperone assisted rna crystallography, phage display, hepatitis a virus, ires, fab antibody, rna-immune system complex, rna/immune system
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 6
• Total formula weight: 167379.86

Authors

Koirala, D.,Shao, Y.,Piccirilli, J.A. (deposition date: 2018-10-29, release date: 2019-08-14, Last modification date: 2024-10-16)

Primary citation

Koirala, D.,Shao, Y.,Koldobskaya, Y.,Fuller, J.R.,Watkins, A.M.,Shelke, S.A.,Pilipenko, E.V.,Das, R.,Rice, P.A.,Piccirilli, J.A.
A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites.
Nat Commun, 10:3629-3629, 2019

PubMed Abstract: Picornaviral IRES elements are essential for initiating the cap-independent viral translation. However, three-dimensional structures of these elements remain elusive. Here, we report a 2.84-Å resolution crystal structure of hepatitis A virus IRES domain V (dV) in complex with a synthetic antibody fragment-a crystallization chaperone. The RNA adopts a three-way junction structure, topologically organized by an adenine-rich stem-loop motif. Despite no obvious sequence homology, the dV architecture shows a striking similarity to a circularly permuted form of encephalomyocarditis virus J-K domain, suggesting a conserved strategy for organizing the domain architecture. Recurrence of the motif led us to use homology modeling tools to compute a 3-dimensional structure of the corresponding domain of foot-and-mouth disease virus, revealing an analogous domain organizing motif. The topological conservation observed among these IRESs and other viral domains implicates a structured three-way junction as an architectural scaffold to pre-organize helical domains for recruiting the translation initiation machinery.

PubMed: 31399592
DOI: 10.1038/s41467-019-11585-z

Experimental method

X-RAY DIFFRACTION (2.838 Å)