Structure of the V protein from <i>parainfluenza virus 5</i> bound to DDB1.

<p>The PDB accession number of the structure is 2HYE. Aa 1–9 and aa 55–80 of V, encompassing the last 2aa of soyuz2, are not visible in the crystal structure, presumably because they are disordered (see text). Soyuz1 is coloured red and soyuz2 blue. The H helix of V, bound to DDB1, is indicated; it partially overlaps with soyuz1.</p

Sequences of <i>Paramyxovirinae</i> P or V proteins.

<p>Sequences of <i>Paramyxovirinae</i> P or V proteins.</p

Alignment of the N-termini of P from <i>respiroviruses</i>.

<p>Positions matching the soyuz1 of the other <i>Paramyxovirinae</i> are indicated above the alignment (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031719#pone-0031719-g002" target="_blank">Figure 2</a>). An experimentally characterized substitution in <i>Sendai virus</i> is in bold.</p

Organization of the <i>Paramyxovirinae</i> P gene.

<p>The P, V and C proteins are encoded from alternative reading frames. V is produced in all <i>Paramyxovirinae</i> genera whereas C is only produced in <i>henipaviruses</i>, <i>morbilliviruses</i>, and <i>respiroviruses</i>.</p

N-termini of P from the <i>rubulaviruses</i>, <i>avulaviruses</i>, and <i>henipaviruses</i> that have the soyuz2 motif.

<p>Conventions as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031719#pone-0031719-g002" target="_blank">Figure 2</a>. (A) Experimentally characterized substitutions in soyuz2 and in the H helix are in bold. (B) Comparison of the N-termini of the V protein of PIV5 and hPIV2 (which both have a soyuz2 motif) with that of hPIV4 (which lacks the soyuz2 motif).</p

Alignment of the N-termini of P from all <i>Paramyxovirinae</i> except <i>respiroviruses</i> (see <b>Figure 3</b>), realized with MAFFT and coloured according to the ClustalX scheme [<b>33</b>].

<p>Abbreviations and accession numbers are in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031719#pone-0031719-t001" target="_blank">Table 1</a>. Positions with conserved physico-chemical character are indicated above the alignment, in bold if the character is strictly conserved (100%) and in normal font if it is generally conserved (>80%). Numbering of the soyuz1 motif (above the alignment) starts at the first strictly conserved position. Unpublished sequences are shown by an asterisk.</p

Sequences of <i>Pneumovirinae</i>, <i>Filoviridae</i>, and <i>Rhabdoviridae</i> P protein.

<p>Sequences of <i>Pneumovirinae</i>, <i>Filoviridae</i>, and <i>Rhabdoviridae</i> P protein.</p

Alignments of the N-termini of P from <i>Pneumovirinae</i>, <i>Filoviridae</i> and <i>Rhabdoviridae</i>.

<p>Conventions as in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031719#pone-0031719-g002" target="_blank">Figure 2</a>. Abbreviations and accession numbers are in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031719#pone-0031719-t002" target="_blank">Table 2</a>. (A) Mir motif of <i>Pneumovirinae</i>. A1 – Alignment of the N-terminus of P of both <i>metapneumoviruses</i> and <i>pneumoviruses</i>. A2 – Same alignment as in A1 but restricted to <i>metapneumoviruses</i>. Positions corresponding to soyuz1 are indicated above the alignment. The coloring of sequence conservation is different from A1 since conservation is now based only on the two <i>metapneumovirus</i> sequences. (B) Sputnik motif of <i>Filoviridae</i>. The asterisk indicates the newly published sequence of <i>LLoviu virus</i>. (C) N-termini of the P of two <i>Rhabdoviridae</i> genera: <i>lyssavirus</i> and <i>vesiculovirus</i>. A disputed L-binding site in <i>lyssavirus</i> P is indicated <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031719#pone.0031719-Chenik1" target="_blank">[108]</a>. The boundaries of the N°-binding region of VSV P were obtained from the crystal structure of N°-P <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031719#pone.0031719-Leyrat3" target="_blank">[58]</a>.</p

Alignment of the first 100aa of all <i>Paramyxovirinae</i> P. Conventions as in <b>Figure 2</b>.

<p>The boundaries of N°-binding regions (underlined in red) have generally been determined indirectly (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0031719#pone-0031719-t003" target="_blank">Table 3</a>), and thus should be taken as approximate. Regions downstream of soyuz1 and soyuz2 (90–330aa in length, of which only ∼50aa are visible on the figure) are unalignable between different genera of <i>Paramyxovirinae</i>.</p

Structural superposition of the C-termini of two <i>Paramyxovirinae</i> and <i>Filoviridae</i> P.

<p>FATCAT superposition between the measles virus X domain (PDB accession number 1T60, chain A), in red, and the <i>Zaire ebolavirus</i> IID domain (3FKE, chain A), in green. N and C refer to N- and C-termini.</p