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Figure 4.
Figure 4. Nucleic acid recognition by RRM domains. a, Stereo
diagram showing the superposition of RRM domains from HuD, Sxl,
PABP, UP1, U1A, and U2B". The bases in all the structures at
positions equivalent to U3/U9 (Sxl, G4/U10; PABP, A3/A6; UP1,
A203/A209; U1A, C10; and U2B", C10) and U4/U10 (Sxl, U5/U11;
PABP, A4/A8; UP1, G204/G210; U1A, A11; and U2B", A11) in the
HuD1,2 -cfos-11 structure are shown in yellow and blue,
respectively. Amino acid side chains at positions equivalent to
Asn 40/Asn 126 (Sxl, Asn 126/Asn 212; PABP, Ser 12/Asn 100; and
UP1, Lys 15/Lys 106), Ile 42/Tyr 128 (Sxl, Ile 124/Tyr 214;
PABP, Tyr 14/Phe 102; UP1, Phe 17/Phe 108; U1A, Tyr 13; and
U2B", Tyr 13), and Phe 84/Phe 170 (Sxl, Phe 170/Phe 256; PABP,
Tyr 56/Phe 142; UP1, Phe 59/Phe 150; U1A, Phe 56; and U2B", Phe
56) in HuD1,2 are shown and backbone atoms at positions
equivalent to Arg 116/Ala 203 of HuD1,2 (Sxl, Arg 202/Ala 289;
PABP, Gln 88/Phe 173; UP1, Val 90/Leu 181; U1A, Lys 88; and
U2B", Lys 88) are shown. Amino acid residues are colored as in
Fig 1b. The side chains of Thr 11 in U1A and U2B", which occupy
positions structurally equivalent to Asn 40/126 of HuD1,2, do
not contact the RNA. Instead the side chains of Ser 91 near the
C-terminus of U1A and U2B", which have no structural equivalent
in the other structures, contact the RNA. b, Base recognition in
the U3/U9 binding pocket. Stereo view showing the superimposed
ball-and-stick models of U3 in the HuD1,2 -cfos-11 structure
(green), G4 in the Sxl -tra structure (yellow), A209 in the UP1
-telomeric DNA structure (blue), and C10 in the U1A -U1 RNA
structure (orange) and the residues contacting the bases. c,
Base recognition in the U4/U10 binding pocket. Stereo view
showing the superimposed ball-and-stick models of U10 in the
HuD1,2 -cfos-11 structure (green), U5 in the Sxl -tra structure
(yellow), A8 in the PABP -A[11] structure (red), and G204 in the
UP1 -telomeric DNA structure (blue) and the residues contacting
the bases. Hydrogen bonds are indicated by dotted lines.
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