3D View: Jmol
Citation Abate-Shen, C., Geiger, J.H., and Hovde, S. (2001), Crystal structure of the Msx-1 homeodomain/DNA complex. Biochemistry 40:12013-12021
[Abstract] [PubMed]
History Deposition: 2001-04-17
Experimental Method X-RAY DIFFRACTION , Resolution: 2.2 Å
Interface to Domain Species Protein Family Superfamily Fold Class
DNA d1ig7a_ Mouse (Mus musculus) [TaxId: 10090] Msx-1 homeodomain Homeodomain Homeodomain-like DNA/RNA-binding 3-helical bundle All alpha proteins
Structural and Functional Restraints Polymer Sequence & Restraints
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Key for HTML output
alpha helix red x
beta sheet blue x
positive phi italic x
solvent accessible upper case x
solvent inaccessible lower case x
disulfide bond cedilla ç
hydrogen bond to DNA orange background & bold x
water-mediated hydrogen bond to DNA orange background & overline x
van der Waals contact to DNA orange background & underline x
hydrogen bond to RNA cyan background & bold x
water-mediated hydrogen bond to RNA cyan background & overline x
van der Waals contact to RNA cyan background & underline x
binding to both DNA and RNA green background & bold x
The Msx-1 homeodomain protein plays a crucial role in craniofacial, limb, and nervous system development. Homeodomain DNA-binding domains are comprised of 60 amino acids that show a high degree of evolutionary conservation. We have determined the structure of the Msx-1 homeodomain complexed to DNA at 2.2 A resolution. The structure has an unusually well-ordered N-terminal arm with a unique trajectory across the minor groove of the DNA. DNA specificity conferred by bases flanking the core TAAT sequence is explained by well ordered water-mediated interactions at Q50. Most interactions seen at the TAAT sequence are typical of the interactions seen in other homeodomain structures. Comparison of the Msx-1-HD structure to all other high resolution HD-DNA complex structures indicate a remarkably well-conserved sphere of hydration between the DNA and protein in these complexes.