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Sci. STKE, 22 April 2003
[DOI: 10.1126/stke.2003.179.re8]

Structures of proline-binding domains interacting with proline-containing peptides. The structures were prepared from Protein Data Bank (PDB) files by Cameron Slayden with the scientific oversight of A. Zarrinpar, R. P. Bhattacharyya, W. A. Lim at the University of California San Francisco, San Francisco, CA.

Structure 1. Structural representation of a polyproline type II (PPII) helix. The helix has twofold pseudosymmetry: A rotation of 180° about a vertical axis leaves the proline rings and the carbonyl oxygens at approximately the same position. The PDB accession code for the poly-(l)-proline structure shown is 1CF0. This animation corresponds to Fig. 1B in the review by Zarrinpar et al.

Structure 2. The structure of the Sem5 SH3 domain in complex with a proline-rich ligand. The core recognition surface has two xP binding grooves formed by aromatic amino acids, shown in yellow, and the adjacent, less conserved specificity pockets are designated in green. The PDB accession code for this structure is 1SEM. This animation corresponds to Fig. 3 in the review by Zarrinpar et al.

Structure 3. The structure of the dystrophin WW domain in complex with a proline-rich ligand. The core recognition surface has one xP binding groove formed by aromatic amino acids (yellow) and adjacent, less conserved specificity pockets (green). The PDB accession code for this structure is 1EG4. This animation corresponds to Fig. 4 in the review by Zarrinpar et al.

Structure 4. A representative structure of the Mena EVH1 domain in complex with a peptide ligand. The apex of the PPII helix fits into an aromatic-rich wedge at the binding surface. Although a conserved set of aromatic residues (yellow) also contacts the PPII ligand, the manner in which the PPII helix docks against the domain surface differs from that observed in most other proline-binding domains discussed here. The PDB accession code for this structure is 1EVH. This animation corresponds to Fig. 5 in the review by Zarrinpar et al.

Structure 5. The structure of the CD2BP2 GYF domain in complex with a proline-rich ligand. The core recognition surface has one xP binding groove formed by aromatic amino acids (yellow) and adjacent, less conserved specificity pockets (green). The PDB accession code for this structure is 1L2Z . This animation corresponds to Fig. 6 in the review by Zarrinpar et al.

Citation: A. Zarrinpar, R. P. Bhattacharyya, W. A. Lim, The structure and function of proline recognition domains. Sci. STKE 2003, re8 (2003).


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Science Signaling. ISSN 1937-9145 (online), 1945-0877 (print). Pre-2008: Science's STKE. ISSN 1525-8882