5UDI

IFIT1 monomeric mutant (L457E/L464E) with m7Gppp-AAAA (syn and anti conformations of cap)

Summary for 5UDI

• Entry DOI: 10.2210/pdb5udi/pdb
• Related: 5UDJ 5UDK 5UDL
• Descriptor: Interferon-induced protein with tetratricopeptide repeats 1, RNA (5'-D(*(GTA))-R(P*AP*AP*A)-3'), TRIETHYLENE GLYCOL, ... (5 entities in total)
• Functional Keywords: mrna cap, n7-methylguanosine-triphosphate rna, tetratricopeptide repeat, rna binding protein
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 57506.74

Authors

Abbas, Y.M.,Martinez-Montero, S.,Damha, M.J.,Nagar, B. (deposition date: 2016-12-27, release date: 2017-03-01, Last modification date: 2024-03-06)

Primary citation

Abbas, Y.M.,Laudenbach, B.T.,Martinez-Montero, S.,Cencic, R.,Habjan, M.,Pichlmair, A.,Damha, M.J.,Pelletier, J.,Nagar, B.
Structure of human IFIT1 with capped RNA reveals adaptable mRNA binding and mechanisms for sensing N1 and N2 ribose 2'-O methylations.
Proc. Natl. Acad. Sci. U.S.A., 114:E2106-E2115, 2017

PubMed Abstract: IFIT1 (IFN-induced protein with tetratricopeptide repeats-1) is an effector of the host innate immune antiviral response that prevents propagation of virus infection by selectively inhibiting translation of viral mRNA. It relies on its ability to compete with the translation initiation factor eIF4F to specifically recognize foreign capped mRNAs, while remaining inactive against host mRNAs marked by ribose 2'-O methylation at the first cap-proximal nucleotide (N1). We report here several crystal structures of RNA-bound human IFIT1, including a 1.6-Å complex with capped RNA. IFIT1 forms a water-filled, positively charged RNA-binding tunnel with a separate hydrophobic extension that unexpectedly engages the cap in multiple conformations ( and ) giving rise to a relatively plastic and nonspecific mode of binding, in stark contrast to eIF4E. Cap-proximal nucleotides encircled by the tunnel provide affinity to compete with eIF4F while allowing IFIT1 to select against N1 methylated mRNA. Gel-shift binding assays confirm that N1 methylation interferes with IFIT1 binding, but in an RNA-dependent manner, whereas translation assays reveal that N1 methylation alone is not sufficient to prevent mRNA recognition at high IFIT1 concentrations. Structural and functional analysis show that 2'-O methylation at N2, another abundant mRNA modification, is also detrimental for RNA binding, thus revealing a potentially synergistic role for it in self- versus nonself-mRNA discernment. Finally, structure-guided mutational analysis confirms the importance of RNA binding for IFIT1 restriction of a human coronavirus mutant lacking viral N1 methylation. Our structural and biochemical analysis sheds new light on the molecular basis for IFIT1 translational inhibition of capped viral RNA.

PubMed: 28251928
DOI: 10.1073/pnas.1612444114

Experimental method

X-RAY DIFFRACTION (1.58 Å)