Supplementary material
for
The bacterial and mitochondrial ribosomal A-site molecular switches
possess different conformational substates.
Jiro Kondo and Eric Westhof*
Architecture et Réactivité de l’ARN, Université Louis Pasteur, Institut de
Biologie Moléculaire et Cellulaire, CNRS, 15 rue René Descartes, 67084
Strasbourg, France.
* To whom correspondence should be addressed:
Tel: +33-3-88-41-70-46
Fax: +33-3-88-60-18-22
Email: [email protected]
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Supplementary figure 1. Secondary (a) and tertiary (b) structures of the RNA duplex in the
asymmetric unit of the BACT-Co crystal. Three universally conserved adenine residues, A1408,
A1492 and A1493, are colored in orange, blue and red, respectively. Two nucleotides different from
those in the H. sapiens mitochondrial A site, U1490 and G1491, are colored in cyan and green,
respectively. Hexamine cobalt cations are colored in pink-blue (ball-and-stick). The unobserved
5’-overhanging uracil residues are shaded in (a).
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Supplementary figure 2. Secondary (a) and tertiary (b) structures of the RNA duplexes in the
asymmetric unit of the WT-K crystal. Three universally conserved adenine residues, A1492, A1557
and A1558 (A1408, A1492 and A1493 in bacterial numbering), are colored in orange, blue and red,
respectively. Two nucleotides different from those in the bacterial A site, A1555 and C1556 (A1490
and C1491 in bacterial numbering), are colored in cyan and green, respectively. The unobserved
5’-overhanging uracil residues are shaded in (a).
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Supplementary figure 3. Secondary (a) and tertiary (b) structures of the RNA duplexes in the
asymmetric unit of the WT-Br-K crystal. Three universally conserved adenine residues, A1492,
A1557 and A1558 (A1408, A1492 and A1493 in bacterial numbering), are colored in orange, blue
and red, respectively. Two nucleotides different from those in the bacterial A site, A1555 and C1556
(A1490 and C1491 in bacterial numbering), are colored in cyan and green, respectively. The
unobserved 5’-overhanging uracil residues are shaded in (a).
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Supplementary figure 4. Secondary (a) and tertiary (b) structures of the RNA duplex in the
asymmetric unit of the MUT-K crystal. Three universally conserved adenine residues, A1492, A1557
and A1558 (A1408, A1492 and A1493 in bacterial numbering), are colored in orange, blue and red,
respectively. Two nucleotides different from those in the bacterial A site, G1555 and C1556 (G1490
and C1491 in bacterial numbering), are colored in cyan and green, respectively. The unobserved
5’-overhanging cytosine residue is shaded in (a).
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Supplementary figure 5. Secondary (a) and tertiary (b) structures of the RNA duplexes in the
asymmetric unit of the MUT-Br1-Sr crystal. Three universally conserved adenine residues, A1492,
A1557 and A1558 (A1408, A1492 and A1493 in bacterial numbering), are colored in orange, blue
and red, respectively. Two nucleotides different from those in the bacterial A site, G1555 and C1556
(G1490 and C1491 in bacterial numbering), are colored in cyan and green, respectively. The
unobserved 5’-overhanging uracil residues are shaded in (a). Hexahydrated strontium ions,
potassium ions and a nonspecifically-bound paromomycin molecule are colored in green-red
(ball-and-stick), violet (ball) and yellow (ball-and-stick), respectively.
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Supplementary figure 6. Secondary (a) and tertiary (b) structures of the RNA duplexes in the
asymmetric unit of the MUT-Br1-K1 crystal. Three universally conserved adenine residues, A1492,
A1557 and A1558 (A1408, A1492 and A1493 in bacterial numbering), are colored in orange, blue
and red, respectively. Two nucleotides different from those in the bacterial A site, G1555 and C1556
(G1490 and C1491 in bacterial numbering), are colored in cyan and green, respectively. The
unobserved 5’-overhanging uracil residues are shaded in (a). Potassium ions and a
nonspecifically-bound paromomycin molecule are colored in violet (ball) and yellow (ball-and-stick),
respectively.
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Supplementary figure 7. Secondary (a) and tertiary (b) structures of the RNA duplexes in the
asymmetric unit of the MUT-Br1-K2 crystal. Three universally conserved adenine residues, A1492,
A1557 and A1558 (A1408, A1492 and A1493 in bacterial numbering), are colored in orange, blue
and red, respectively. Two nucleotides different from those in the bacterial A site, G1555 and C1556
(G1490 and C1491 in bacterial numbering), are colored in cyan and green, respectively. The
unobserved 5’-overhanging uracil residues are shaded in (a). Potassium ions are colored in violet
(ball).
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Supplementary figure 8. Secondary (a) and tertiary (b) structures of the RNA duplex in the
asymmetric unit of the MUT-Br2-Co crystal. Three universally conserved adenine residues, A1492,
A1557 and A1558 (A1408, A1492 and A1493 in bacterial numbering), are colored in orange, blue
and red, respectively. Two nucleotides different from those in the bacterial A site, G1555 and C1556
(G1490 and C1491 in bacterial numbering), are colored in cyan and green, respectively. Hexammine
cobalt cations and sodium ions are colored in pink-blue (ball-and-stick) and violet (ball),
respectively.
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Supplementary figure 9. Secondary and superimposed tertiary structures of the bacterial “off” state
(a), the mitochondrial wild-type “off” state (b) and the first and second conformations of the
A1555G mutant “off” state (c, d) found in the present crystal structures.
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Supplementary figure 10. Secondary and tertiary structures of the bacterial “off” and “on” states (a),
the H. sapiens mitochondrial wild-type “off” state (b) and the first and second conformation of the
A1555G mutant “off” states (c, d). Base-stacking columns are colored in red, blue, orange and green,
respectively. Bases, which are not involved in any stacking column, are colored in gray.
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Supplementary figure 11. Overview of the A-site molecular switches of the bacterial, mitochondrial
wild-type and its A1555G mutant. Base-stacking columns are colored in red, blue, orange and green,
respectively. Bases, which are not involved in any stacking column, are colored in gray.
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