1xjy
From Proteopedia
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|PDB= 1xjy |SIZE=350|CAPTION= <scene name='initialview01'>1xjy</scene>, resolution 2.00Å | |PDB= 1xjy |SIZE=350|CAPTION= <scene name='initialview01'>1xjy</scene>, resolution 2.00Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= | + | |LIGAND= <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5'-MONOPHOSPHATE'>DT</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1xjx|1XJX]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1xjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjy OCA], [http://www.ebi.ac.uk/pdbsum/1xjy PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1xjy RCSB]</span> | ||
}} | }} | ||
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[[Category: runx1]] | [[Category: runx1]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:50:41 2008'' |
Revision as of 21:50, 30 March 2008
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| , resolution 2.00Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , | ||||||
| Related: | 1XJX
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| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
The crystal structures of the DNA binding sites of the RUNX1 transcription factor
Overview
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.
About this Structure
1XJY is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structures of the DNA-binding site of Runt-domain transcription regulators., Kitayner M, Rozenberg H, Rabinovich D, Shakked Z, Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):236-46. Epub 2005, Feb 24. PMID:15735333
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