Structural role of a detergent molecule in retinoic acid nuclear receptor crystals

Klaholz, B.P.; Moras, D.

doi:10.1107/S090744490000634X

Figure 2
(a) The dodecyl-α-D-maltoside molecule (in yellow) mediating a crystal contact between two molecules of the hRARγ LBD/CD564 complex (space group P4₁2₁2; symmetry operators x − $[1\over2]$ , −y + $[3\over2]$ , −z + $[3\over4]$ ). The retinoid CD564 is shown in red. H1 to H12 denote helices and N and C denote the N- and C-termini of the protein, respectively. (b) GRASP representation of the cavity. 83% of the detergent molecule surface are buried within the crystal contact. Calculations of excluded areas were performed with GRASP (Nicholls et al., 1991

). (c) The σ_A-weighted F_o − F_c omit map (coloured orange; stereo representation) at 1.30 Å resolution is contoured at 2.5σ and reveals the bent shape of the dodecyl-α-D-maltoside molecule. The dodecyl moiety is buried in a hydrophobic channel generated by helices H3, H4 and H12 of hRARγ (coloured green) and loop L8/9 and helices H9 and H10 of hRARγ_sym (coloured blue). The O atoms of the detergent are coloured red and the C atoms grey. Hydrophobic side chains are indicated in grey, water molecules in blue and the mercury-binding cysteines in pink. The double conformation of Cys267 is shown in yellow. The positions of Lys246, Lys264 and Glu414 can be compared with those described in Fig. 3

. Figs. 2(a), 2(c) and 3 were created with SETOR (Evans, 1993

BIOLOGICAL
CRYSTALLOGRAPHY

ISSN: 1399-0047

Volume 56| Part 7| July 2000| Pages 933-935

doi:10.1107/S090744490000634X

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