3ABN

Crystal structure of (Pro-Pro-Gly)4-Hyp-Asp-Gly-(Pro-Pro-Gly)4 at 1.02 A

Summary for 3ABN

• Entry DOI: 10.2210/pdb3abn/pdb
• Related: 2DRT 2DRX 3A08 3A0M 3A19
• Descriptor: collagen-like peptide (2 entities in total)
• Functional Keywords: collagen-helix, structural protein
• Total number of polymer chains: 3
• Total formula weight: 6940.56

Authors

Okuyama, K.,Shimura, M.,Kawaguchi, T.,Noguchi, K.,Mizuno, K.,Bachinger, H.P. (deposition date: 2009-12-16, release date: 2010-12-01, Last modification date: 2025-03-26)

Primary citation

Okuyama, K.,Kawaguchi, T.,Shimura, M.,Noguchi, K.,Mizuno, K.,Bachinger, H.P.
Crystal structure of the collagen model peptide (Pro-Pro-Gly)4 -Hyp-Asp-Gly-(Pro-Pro-Gly)4 at 1.0 angstrom resolution.
Biopolymers, 99:436-447, 2013

PubMed Abstract: The single-crystal structure of the collagen-like peptide (Pro-Pro-Gly)4 -Hyp-Asp-Gly-(Pro-Pro-Gly)4, was analyzed at 1.02 Å resolution. The overall average helical twist (θ = 49.6°) suggests that this peptide adopts a 7/2 triple-helical structure and that its conformation is very similar to that of (Gly-Pro-Hyp)9, which has the typical repeating sequence in collagen. High-resolution studies on other collagen-like peptides have shown that imino acid-rich sequences preferentially adopt a 7/2 triple-helical structure (θ = 51.4°), whereas imino acid-lean sequences adopt relaxed conformations (θ < 51.4°). The guest Gly-Hyp-Asp sequence in the present peptide, however, has a large helical twist (θ = 61.1°), whereas that of the host Pro-Pro-Gly sequence is small (θ = 46.7°), indicating that the relationship between the helical conformation and the amino acid sequence of such peptides is complex. In the present structure, a strong intermolecular hydrogen bond between two Asp residues on the A and B strands might induce the large helical twist of the guest sequence; this is compensated by a reduced helical twist in the host, so that an overall 7/2-helical symmetry is maintained. The Asp residue in the C strand might interact electrostatically with the N-terminus of an adjacent molecule, causing axial displacement, reminiscent of the D-staggered structure in fibrous collagens.

PubMed: 23616212
DOI: 10.1002/bip.22198

Experimental method

X-RAY DIFFRACTION (1.02 Å)