Research ArticleVIROLOGY

Near-atomic structure of an atadenovirus reveals a conserved capsid-binding motif and intergenera variations in cementing proteins

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Science Advances  31 Mar 2021:
Vol. 7, no. 14, eabe6008
DOI: 10.1126/sciadv.abe6008
  • Fig. 1 LAdV-2 cryo-EM map and molecular model.

    (A) Right: Surface rendering of the LAdV-2 three-dimensional (3D) map colored by radius from white to pink, as indicated by the color scale. A zoom-in on the area corresponding to the icosahedral asymmetric unit (AU) is shown at the right. The four hexon trimers in an AU are numbered 1 to 4. White symbols indicate the icosahedral fivefold (pentagon), threefold (triangle), and twofold (oval) symmetry axes. (B) Ribbon representation of the proteins traced in the AU, colored as indicated by the legend at the left. Depth cueing (fading to white) is used to give an impression of distance to the viewer. Two views are provided, as seen from outside (top) or inside (bottom) the capsid, with a cartoon at the right-hand side for guidance. In the cartoon, icosahedral symmetry axes are indicated by red symbols.

  • Fig. 2 LAdV-2 main capsid proteins: hexon and penton.

    (A) Hexon trimer as seen from inside (left) or outside (center) the capsid and in a side view (right). The capsomer base and towers are indicated, as well as the N terminus (N) and C terminus (C) of each monomer. The two β barrels forming the double jelly roll are labeled P1 and P2. (B) Superposition of the LAdV-2 and HAdV-C5 (PDB ID 6B1T) hexon monomers. The length in residues of the HAdV-C5 untraced loops is indicated. (C) Superposition of the 12 hexon monomers in the LAdV-2 AU, colored by RMSD according to the scale at the right-hand side. MR1 and MR2: mobile regions. (D) Penton base pentamer as seen from outside the capsid (top) and in a side view (bottom). The N terminus of one monomer and the location of the EGD sequence are indicated. (E) Superposition of the LAdV-2 and HAdV-C5 penton base monomers. The length in residues (res) of the HAdV-C5 penton RGD loop is indicated. (F) Interactions of one penton base monomer with other proteins. AU_1 and AU_7 indicate molecules in neighboring AUs labeled as in fig. S3.

  • Fig. 3 Schematics illustrating the LAdV-2 protein networks.

    Hexons 1 to 4 in one AU are depicted in white and labeled with black text; those in neighboring AUs in the same icosahedral facet are in white with gray labels; and those in adjacent facets are in gray. Letters A to L identify different polypeptide chains as in tables S2 to S9. Red symbols indicate the icosahedral fivefold (pentagon), threefold (triangle), and twofold (oval) symmetry axes. Closed and broken white triangles indicate two different local threefold symmetry axes. (A) Hexon conformational adaptability: location of mobile hexon regions in the capsid. Hexon mobile regions MR1 and MR2 in one AU and its immediate neighbors are indicated. A few hexon N and C termini are depicted as an example. In the hexon schematics legend, S designates the facet of the hexon pseudo-hexagonal base formed by the two β barrels in a single monomer, and T indicates the facet of the hexon pseudo-hexagonal base formed by two β barrels belonging to two adjacent hexon monomers (1). (B) Location of the minor coat proteins. Only LH3 is located on the outer capsid surface.

  • Fig. 4 LAdV-2 external minor coat proteins: LH3.

    (A) Superposition of the LAdV-2 and SnAdV-1 (PDB ID 5G5O) LH3 structures. The first (Val4 and Ser26) and last (Pro370 and Ala373) residues traced for each protein are indicated. Asn157 is labeled to indicate the location of the Asp155-Ser162 loop mentioned in the text. (B) Overall view of the LH3 trimer seen from outside the capsid (left) and in a side view (right). The N and C termini of the pink subunit are labeled, as well as the β helix, column and triskelion domains. (C) Hexons 2 and 3 are represented to show the LH3 trimer in the capsid context. The monomers in each neighboring hexon trimer are colored light blue, light pink, and tan. (D) Comparison between the triskelions formed by LAdV-2 LH3 and HAdV-C5 protein IX, in a side view similar to (C). (E) As in (D), but in a view from the capsid surface. In this view, the LH3 column domains would travel away from the reader. (F) LH3 trimer overlapped with the HAdV-C5 protein IX trimer, to show the large difference in the fold beyond the triskelion domain. The C terminus for one monomer of IX and one monomer of LH3 are labeled.

  • Fig. 5 Comparison of the E1B-55 K/LH3 locus in the family Adenoviridae.

    (A) Genome alignment of AdVs representing the five genera currently recognized. The genomes are indicated with the corresponding GenBank accession numbers and the abbreviated names of the genera, Ichtadenovirus, Siadenovirus, Aviadenovirus, Atadenovirus, and Mastadenovirus. In each case, only the left extremity of the genome which in atadenoviruses and mastadenoviruses encompasses the E1B-55 K/LH3 genes is shown. The genomes are aligned according to the gene encoding the IVa2 protein. Homologous genes are colored with the same color and, in the case of E1B-55 K/LH3 homologs, are connected by light green shading. Note that mastadenovirus equine AdV 2 (NC_027705) encodes two copies of E1B-55 K/LH3 homologs. The schematic cladogram on the left represents the established phylogenetic relationships within the family Adenoviridae (39). DNAP: DNA polymerase; pTP: pre-terminal protein; dUTPase: deoxyuridine-triphosphatase; kbp: kilo-basepair. (B) Domain organization of the E1B-55 K/LH3 homologs in LAdV-2 (Atadenovirus) and two mastadenoviruses, equine AdV 2 and human mastadenovirus C. The Pfam domain Adeno_E1B_55K (accession number PF01696.18) and the triskelion domain (Trisk) are colored with different shades of green.

  • Fig. 6 LAdV-2 internal minor coat proteins: VIII and IIIa.

    (A) Superposition of the LAdV-2 and HAdV-C5 protein VIII structures. The body, neck, and head domains are indicated, as well as the positions of the N- and C-terminal residues in the structure and the residues flanking the central gap. (B) A view from inside the capsid along a fivefold axis showing the ring of protein IIIa. One copy of IIIa is highlighted in vivid yellow. (C) Structure of the IIIa monomer. The GOS-glue and VIII-binding domains, as well as the connecting helix, the first and last residues traced, and those flanking the connecting helix are indicated. (D) Comparison between the LAdV-2 (yellow) and HAdV-C5 (gray) protein IIIa structures, presented in their original position in the capsid, in which the GOS-glue domains and part of the connecting helix overlap. Three points of view are shown, and angles between the connecting helices and between the first helix in the VIII-binding domain of each protein (α7) are indicated. (E) Superposition of the two VIII-binding domains showing the fold similarity. (F) LAdV-2 vertex proteins depicted together with HAdV-C5 protein IIIa, to show the effect of the large conformational change on its interactions with protein VIII.

  • Fig. 7 Unassigned elements on the LAdV-2 internal capsid surface.

    (A) Peptides modeled in the U1 density. Numbers in parentheses indicate the peptide lengths in amino acids. (B) View of the U1 peptides in the capsid context. The star indicates the location of the gap left by maturation cleavages in protein VIII. Hexon 2, which would be in front, has been removed for clarity. (C) Peptides modeled in the U2 density (magenta) form an interlaced ring with IIIa beneath the vertex. View along the fivefold symmetry axis from inside the capsid. (D) The U2 peptides are intercalated between IIIa and the body domain of VIII (top). If IIIa adopted the same conformation as in HAdV-C5, it would badly clash with U2 (bottom).

Supplementary Materials

  • Supplementary Materials

    Near-atomic structure of an atadenovirus reveals a conserved capsid-binding motif and intergenera variations in cementing proteins

    Roberto Marabini, Gabriela N. Condezo, Mart Krupovic, Rosa Menéndez-Conejero, Josué Gómez-Blanco, Carmen San Martín

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    • Figs. S1 to S10
    • Tables S1 to S11
    • Legend for data file S1

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