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| - | [[Image:1xjy.gif|left|200px]] | |
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| - | {{Structure
| + | ==The crystal structures of the DNA binding sites of the RUNX1 transcription factor== |
| - | |PDB= 1xjy |SIZE=350|CAPTION= <scene name='initialview01'>1xjy</scene>, resolution 2.00Å
| + | <StructureSection load='1xjy' size='340' side='right'caption='[[1xjy]], [[Resolution|resolution]] 2.00Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |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>
| + | <table><tr><td colspan='2'>[[1xjy]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1XJY FirstGlance]. <br> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2Å</td></tr> |
| - | |GENE=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1xjy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1xjy OCA], [https://pdbe.org/1xjy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1xjy RCSB], [https://www.ebi.ac.uk/pdbsum/1xjy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1xjy ProSAT]</span></td></tr> |
| - | |DOMAIN=
| + | </table> |
| - | |RELATEDENTRY=[[1xjx|1XJX]]
| + | __TOC__ |
| - | |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>
| + | </StructureSection> |
| - | }}
| + | [[Category: Large Structures]] |
| - | | + | [[Category: Kitayner M]] |
| - | '''The crystal structures of the DNA binding sites of the RUNX1 transcription factor'''
| + | [[Category: Rabinovich D]] |
| - | | + | [[Category: Rozenberg H]] |
| - | | + | [[Category: Shakked Z]] |
| - | ==Overview==
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| - | 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.
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| - | ==About this Structure==
| + | |
| - | 1XJY is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1XJY OCA].
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| - | ==Reference==
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| - | 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:[http://www.ncbi.nlm.nih.gov/pubmed/15735333 15735333]
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| - | [[Category: Protein complex]] | + | |
| - | [[Category: Kitayner, M.]] | + | |
| - | [[Category: Rabinovich, D.]] | + | |
| - | [[Category: Rozenberg, H.]] | + | |
| - | [[Category: Shakked, Z.]] | + | |
| - | [[Category: a-dna]]
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| - | [[Category: double helix]]
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| - | [[Category: overhanging base]]
| + | |
| - | [[Category: runx1]]
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| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:50:41 2008''
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