1ckt

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{{Seed}}
 
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[[Image:1ckt.png|left|200px]]
 
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==CRYSTAL STRUCTURE OF HMG1 DOMAIN A BOUND TO A CISPLATIN-MODIFIED DNA DUPLEX==
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The line below this paragraph, containing "STRUCTURE_1ckt", creates the "Structure Box" on the page.
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<StructureSection load='1ckt' size='340' side='right'caption='[[1ckt]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1ckt]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CKT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CKT FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</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>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=CPT:CISPLATIN'>CPT</scene></td></tr>
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{{STRUCTURE_1ckt| PDB=1ckt | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ckt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ckt OCA], [https://pdbe.org/1ckt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ckt RCSB], [https://www.ebi.ac.uk/pdbsum/1ckt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ckt ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/HMGB1_RAT HMGB1_RAT] DNA binding proteins that associates with chromatin and has the ability to bend DNA. Binds preferentially single-stranded DNA. Involved in V(D)J recombination by acting as a cofactor of the RAG complex. Acts by stimulating cleavage and RAG protein binding at the 23 bp spacer of conserved recombination signal sequences (RSS). Heparin-binding protein that has a role in the extension of neurite-type cytoplasmic processes in developing cells (By similarity).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ck/1ckt_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1ckt ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The anticancer activity of cis-diamminedichloroplatinum(II) (cisplatin) arises from its ability to damage DNA, with the major adducts formed being intrastrand d(GpG) and d(ApG) crosslinks. These crosslinks bend and unwind the duplex, and the altered structure attracts high-mobility-group domain (HMG) and other proteins. This binding of HMG-domain proteins to cisplatin-modified DNA has been postulated to mediate the antitumour properties of the drug. Many HMG-domain proteins recognize altered DNA structures such as four-way junctions and cisplatin-modified DNA, but until now the molecular basis for this recognition was unknown. Here we describe mutagenesis, hydroxyl-radical footprinting and X-ray studies that elucidate the structure of a 1:1 cisplatin-modified DNA/HMG-domain complex. Domain A of the structure-specific HMG-domain protein HMG1 binds to the widened minor groove of a 16-base-pair DNA duplex containing a site-specific cis-[Pt(NH3)2[d(GpG)-N7(1),-N7(2)]] adduct. The DNA is strongly kinked at a hydrophobic notch created at the platinum-DNA crosslink and protein binding extends exclusively to the 3' side of the platinated strand. A phenylalanine residue at position 37 intercalates into a hydrophobic notch created at the platinum crosslinked d(GpG) site and binding of the domain is dramatically reduced in a mutant in which alanine is substituted for phenylalanine at this position.
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===CRYSTAL STRUCTURE OF HMG1 DOMAIN A BOUND TO A CISPLATIN-MODIFIED DNA DUPLEX===
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Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins.,Ohndorf UM, Rould MA, He Q, Pabo CO, Lippard SJ Nature. 1999 Jun 17;399(6737):708-12. PMID:10385126<ref>PMID:10385126</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 1ckt" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_10385126}}, adds the Publication Abstract to the page
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*[[High mobility group protein|High mobility group protein]]
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(as it appears on PubMed at http://www.pubmed.gov), where 10385126 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_10385126}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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1CKT is a 3 chains structure of sequences from [http://en.wikipedia.org/wiki/Rattus_norvegicus Rattus norvegicus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CKT OCA].
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==Reference==
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<ref group="xtra">PMID:10385126</ref><references group="xtra"/>
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[[Category: Rattus norvegicus]]
[[Category: Rattus norvegicus]]
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[[Category: Lippard, S J.]]
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[[Category: Lippard SJ]]
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[[Category: Ohndorf, U M.]]
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[[Category: Ohndorf U-M]]
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[[Category: Pabo, C O.]]
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[[Category: Pabo CO]]
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[[Category: Rould, M A.]]
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[[Category: Rould MA]]
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[[Category: Bent dna]]
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[[Category: High-mobility group domain]]
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[[Category: Protein-drug-dna complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 17:49:14 2009''
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Current revision

CRYSTAL STRUCTURE OF HMG1 DOMAIN A BOUND TO A CISPLATIN-MODIFIED DNA DUPLEX

PDB ID 1ckt

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