1ljm: Difference between revisions

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-{{Seed}}
-[[Image:1ljm.png|left|200px]]
-<!--
+==DNA recognition is mediated by conformational transition and by DNA bending==
-The line below this paragraph, containing "STRUCTURE_1ljm", creates the "Structure Box" on the page.
+<StructureSection load='1ljm' size='340' side='right'caption='[[1ljm]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1ljm]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LJM FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-{{STRUCTURE_1ljm|  PDB=1ljm  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ljm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ljm OCA], [https://pdbe.org/1ljm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ljm RCSB], [https://www.ebi.ac.uk/pdbsum/1ljm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ljm ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/RUNX1_HUMAN RUNX1_HUMAN] Note=A chromosomal aberration involving RUNX1/AML1 is a cause of M2 type acute myeloid leukemia (AML-M2). Translocation t(8;21)(q22;q22) with RUNX1T1.<ref>PMID:1423235</ref> <ref>PMID:8353289</ref> <ref>PMID:8334990</ref> <ref>PMID:7919324</ref> <ref>PMID:7541640</ref>   Note=A chromosomal aberration involving RUNX1/AML1 is a cause of therapy-related myelodysplastic syndrome (T-MDS). Translocation t(3;21)(q26;q22) with EAP or MECOM.  Note=A chromosomal aberration involving RUNX1/AML1 is a cause of chronic myelogenous leukemia (CML). Translocation t(3;21)(q26;q22) with EAP or MECOM.  Note=A chromosomal aberration involving RUNX1/AML1 is found in childhood acute lymphoblastic leukemia (ALL). Translocation t(12;21)(p13;q22) with TEL. The translocation fuses the 3'-end of TEL to the alternate 5'-exon of AML-1H.  Note=A chromosomal aberration involving RUNX1 is found in acute leukemia. Translocation t(11,21)(q13;q22) that forms a MACROD1-RUNX1 fusion protein.  Defects in RUNX1 are the cause of familial platelet disorder with associated myeloid malignancy (FPDMM) [MIM:[https://omim.org/entry/601399 601399]. FPDMM is an autosomal dominant disease characterized by qualitative and quantitative platelet defects, and propensity to develop acute myelogenous leukemia.<ref>PMID:10508512</ref>   Note=A chromosomal aberration involving RUNX1/AML1 is found in therapy-related myeloid malignancies. Translocation t(16;21)(q24;q22) that forms a RUNX1-CBFA2T3 fusion protein.  Note=A chromosomal aberration involving RUNX1/AML1 is a cause of chronic myelomonocytic leukemia. Inversion inv(21)(q21;q22) with USP16.
+== Function ==
+[https://www.uniprot.org/uniprot/RUNX1_HUMAN RUNX1_HUMAN] CBF binds to the core site, 5'-PYGPYGGT-3', of a number of enhancers and promoters, including murine leukemia virus, polyomavirus enhancer, T-cell receptor enhancers, LCK, IL-3 and GM-CSF promoters. The alpha subunit binds DNA and appears to have a role in the development of normal hematopoiesis. Isoform AML-1L interferes with the transactivation activity of RUNX1. Acts synergistically with ELF4 to transactivate the IL-3 promoter and with ELF2 to transactivate the mouse BLK promoter. Inhibits KAT6B-dependent transcriptional activation.<ref>PMID:10207087</ref> <ref>PMID:11965546</ref> <ref>PMID:14970218</ref> <ref>PMID:17431401</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/lj/1ljm_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ljm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The Runt domain proteins are transcription regulators of major developmental pathways. Here we present the crystal structures of the Runt domain (RD) of the human protein RUNX1 and its DNA binding site in their free states and compare them with the published crystal structures of RD bound to DNA and to the partner protein CBFbeta. We demonstrate that (1) RD undergoes an allosteric transition upon DNA binding, which is further stabilized by CBFbeta, and that (2) the free DNA target adopts a bent-helical conformation compatible with that of the complex. These findings elucidate the mechanism by which CBFbeta enhances RD binding to DNA as well as the role of the intrinsic conformation of the DNA target in the recognition process.
-===DNA recognition is mediated by conformational transition and by DNA bending===
+DNA recognition by the RUNX1 transcription factor is mediated by an allosteric transition in the RUNT domain and by DNA bending.,Bartfeld D, Shimon L, Couture GC, Rabinovich D, Frolow F, Levanon D, Groner Y, Shakked Z Structure. 2002 Oct;10(10):1395-407. PMID:12377125<ref>PMID:12377125</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ljm" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_12377125}}, adds the Publication Abstract to the page
+*[[Core-binding factor|Core-binding factor]]
-(as it appears on PubMed at http://www.pubmed.gov), where 12377125 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_12377125}}
+__TOC__
+</StructureSection>
-==About this Structure==
-LJM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LJM OCA].
-==Reference==
-DNA recognition by the RUNX1 transcription factor is mediated by an allosteric transition in the RUNT domain and by DNA bending., Bartfeld D, Shimon L, Couture GC, Rabinovich D, Frolow F, Levanon D, Groner Y, Shakked Z, Structure. 2002 Oct;10(10):1395-407. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12377125 12377125]
 [[Category: Homo sapiens]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Bartfeld, D.]]
+[[Category: Bartfeld D]]
-[[Category: Couture, G C.]]
+[[Category: Couture GC]]
-[[Category: Frolow, F.]]
+[[Category: Frolow F]]
-[[Category: Groner, Y.]]
+[[Category: Groner Y]]
-[[Category: Levanon, D.]]
+[[Category: Levanon D]]
-[[Category: Rabinovich, D.]]
+[[Category: Rabinovich D]]
-[[Category: Shakked, Z.]]
+[[Category: Shakked Z]]
-[[Category: Shimon, L.]]
+[[Category: Shimon L]]
-[[Category: Beta-sandwich]]
-[[Category: Immunoglobulin fold]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  2 21:01:29 2008''