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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Crystal structure of a highly conserved enteroviral 5' cloverleaf RNA replication element

The extreme 5'-end of the enterovirus RNA genome contains a conserved cloverleaf-like domain that recruits 3CD and PCBP proteins required for initiating genome replication. Here, we report the crystal structure at 1.9 Å resolution of this domain from the CVB3 genome in complex with an antibody chaperone. The RNA folds into an antiparallel H-type four-way junction comprising four subdomains with co-axially stacked sA-sD and sB-sC helices. Long-range interactions between a conserved A40 in the sC-loop and Py-Py helix within the sD subdomain organize near-parallel orientations of the sA-sB and sC-sD helices. Our NMR studies confirm that these long-range interactions occur in solution and without the chaperone. The phylogenetic analyses indicate that our crystal structure represents a conserved architecture of enteroviral cloverleaf-like domains, including the A40 and Py-Py interactions. The protein binding studies further suggest that the H-shape architecture provides a ready-made platform to recruit 3CD and PCBP2 for viral replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural basis for a highly conserved RNA-mediated enteroviral genome replication

Abstract Enteroviruses contain conserved RNA structures at the extreme 5′ end of their genomes that recruit essential proteins 3CD and PCBP2 to promote genome replication. However, the high-resolution structures and mechanisms of these replication-linked RNAs (REPLRs) are limited. Here, we determined the crystal structures of the coxsackievirus B3 and rhinoviruses B14 and C15 REPLRs at 1.54, 2.2 and 2.54 Å resolution, revealing a highly conserved H-type four-way junction fold with co-axially stacked sA-sD and sB-sC helices that are stabilized by a long-range A•C•U base-triple. Such conserved features observed in the crystal structures also allowed us to predict the models of several other enteroviral REPLRs using homology modeling, which generated models almost identical to the experimentally determined structures. Moreover, our structure-guided binding studies with recombinantly purified full-length human PCBP2 showed that two previously proposed binding sites, the sB-loop and 3′ spacer, reside proximally and bind a single PCBP2. Additionally, the DNA oligos complementary to the 3′ spacer, the high-affinity PCBP2 binding site, abrogated its interactions with enteroviral REPLRs, suggesting the critical roles of this single-stranded region in recruiting PCBP2 for enteroviral genome replication and illuminating the promising prospects of developing therapeutics against enteroviral infections targeting this replication platform.

Biochemistry & Molecular Biology↗
DOE OSTI2020

Materials Data on ScSb by Materials Project

ScSb is Tetraauricupride structured and crystallizes in the cubic Pm-3m space group. The structure is three-dimensional. Sc3+ is bonded in a body-centered cubic geometry to eight equivalent Sb3- atoms. All Sc–Sb bond lengths are 3.14 Å. Sb3- is bonded in a body-centered cubic geometry to eight equivalent Sc3+ atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on ScSb by Materials Project

ScSb is Halite, Rock Salt structured and crystallizes in the cubic Fm-3m space group. The structure is three-dimensional. Sc3+ is bonded to six equivalent Sb3- atoms to form a mixture of edge and corner-sharing ScSb6 octahedra. The corner-sharing octahedral tilt angles are 0°. All Sc–Sb bond lengths are 2.95 Å. Sb3- is bonded to six equivalent Sc3+ atoms to form a mixture of edge and corner-sharing SbSc6 octahedra. The corner-sharing octahedral tilt angles are 0°.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Sc2Sb by Materials Project

Sc2Sb crystallizes in the tetragonal P4/nmm space group. The structure is three-dimensional. there are two inequivalent Sc sites. In the first Sc site, Sc is bonded in a 12-coordinate geometry to four equivalent Sb atoms. All Sc–Sb bond lengths are 3.05 Å. In the second Sc site, Sc is bonded to five equivalent Sb atoms to form a mixture of distorted edge and corner-sharing ScSb5 square pyramids. There are one shorter (2.95 Å) and four longer (3.03 Å) Sc–Sb bond lengths. Sb is bonded in a 9-coordinate geometry to nine Sc atoms.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on Sc3Sb by Materials Project

Sc3Sb is Uranium Silicide-like structured and crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. there are two inequivalent Sc sites. In the first Sc site, Sc is bonded to eight Sc and four equivalent Sb atoms to form distorted ScSc8Sb4 cuboctahedra that share corners with twelve equivalent ScSc8Sb4 cuboctahedra, edges with eight equivalent ScSc8Sb4 cuboctahedra, edges with eight equivalent SbSc12 cuboctahedra, faces with four equivalent SbSc12 cuboctahedra, and faces with ten equivalent ScSc8Sb4 cuboctahedra. There are four shorter (3.07 Å) and four longer (3.27 Å) Sc–Sc bond lengths. All Sc–Sb bond lengths are 3.27 Å. In the second Sc site, Sc is bonded in a square co-planar geometry to eight equivalent Sc and four equivalent Sb atoms. All Sc–Sb bond lengths are 3.07 Å. Sb is bonded to twelve Sc atoms to form SbSc12 cuboctahedra that share corners with four equivalent SbSc12 cuboctahedra, edges with eight equivalent SbSc12 cuboctahedra, edges with sixteen equivalent ScSc8Sb4 cuboctahedra, faces with four equivalent SbSc12 cuboctahedra, and faces with eight equivalent ScSc8Sb4 cuboctahedra.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Materials Data on ScSb3 by Materials Project

ScSb3 crystallizes in the hexagonal P6_3/mmc space group. The structure is three-dimensional. Sc3+ is bonded to twelve equivalent Sb1- atoms to form a mixture of face and corner-sharing ScSb12 cuboctahedra. There are six shorter (3.25 Å) and six longer (3.34 Å) Sc–Sb bond lengths. Sb1- is bonded in a 4-coordinate geometry to four equivalent Sc3+ atoms.

36 MATERIALS SCIENCE↗