1XJX

The crystal structures of the DNA binding sites of the RUNX1 transcription factor

Summary for 1XJX

• Entry DOI: 10.2210/pdb1xjx/pdb
• Related: 1XJY
• Descriptor: 5'-D(*TP*CP*TP*GP*CP*GP*GP*TP*C)-3', 5'-D(*TP*GP*AP*CP*CP*GP*CP*AP*G)-3' (3 entities in total)
• Functional Keywords: a-dna, double helix, overhanging bases, runx1, dna
• Total number of polymer chains: 2
• Total formula weight: 5463.60

Authors

Kitayner, M.,Rozenberg, H.,Rabinovich, D.,Shakked, Z. (deposition date: 2004-09-26, release date: 2005-03-15, Last modification date: 2024-04-03)

Primary citation

Kitayner, M.,Rozenberg, H.,Rabinovich, D.,Shakked, Z.
Structures of the DNA-binding site of Runt-domain transcription regulators.
Acta Crystallogr.,Sect.D, 61:236-246, 2005

PubMed Abstract: Runt-domain (RD) proteins are transcription factors that play fundamental roles in various developmental pathways. They bind specifically to DNA sequences of the general form PyGPyGGTPy (Py = pyrimidine), through which they regulate transcription of target genes. The DNA duplex TCTGCGGTC/TGACCGCAG, incorporating the binding site for the RD transcription factors (bold), was crystallized in space group P4(3). X-ray analysis of two crystals diffracting to 1.7 and 2.0 angstroms resolution, which had slight variations in their unit-cell parameters, revealed two distinct conformations of the A-DNA helix. The two crystal structures possessed several structure and hydration features that had previously been observed in A-DNA duplexes. A comparative analysis of the present A-DNA structures and those of previously reported B-DNA crystal structures of RD-binding sites in free and protein-bound states showed the various duplexes to display several common features. Within this series, the present A-DNA duplexes adopt two conformations along the pathway from the canonical A-DNA to the B-DNA forms and the protein-bound helices display conformational features that are intermediate between those of the current A-DNA structures and that of the B-DNA-type helix of the free RD target. Based on these data and energy considerations, it is likely that the propensity of the RD-binding site to adopt the A-DNA or B-DNA conformation in solution depends on the sequence context and environmental conditions, and that the transition from either DNA form to the protein-bound conformation involves a small energy barrier.

PubMed: 15735333
DOI: 10.1107/S0907444904032378

Experimental method

X-RAY DIFFRACTION (1.7 Å)