1pib: Difference between revisions

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{{Seed}}
[[Image:1pib.png|left|200px]]


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==Solution structure of DNA containing CPD opposited by GA==
The line below this paragraph, containing "STRUCTURE_1pib", creates the "Structure Box" on the page.
<StructureSection load='1pib' size='340' side='right'caption='[[1pib]]' 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'>[[1pib]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PIB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PIB 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">Solution NMR</td></tr>
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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=1pib FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pib OCA], [https://pdbe.org/1pib PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pib RCSB], [https://www.ebi.ac.uk/pdbsum/1pib PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pib ProSAT]</span></td></tr>
{{STRUCTURE_1pib|  PDB=1pib  |  SCENE=  }}
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The cis-syn cyclobutane pyrimidine dimer (CPD) is a cytotoxic, mutagenic and carcinogenic DNA photoproduct and is repaired by the nucleotide excision repair (NER) pathway in mammalian cells. The XPC-hHR23B complex as the initiator of global genomic NER binds to sites of certain kinds of DNA damage. Although CPDs are rarely recognized by the XPC-hHR23B complex, the presence of mismatched bases opposite a CPD significantly increased the binding affinity of the XPC-hHR23B complex to the CPD. In order to decipher the properties of the DNA structures that determine the binding affinity for XPC-hHR23B to DNA, we carried out structural analyses of the various types of CPDs by NMR spectroscopy. The DNA duplex which contains a single 3' T*G wobble pair in a CPD (CPD/GA duplex) induces little conformational distortion. However, severe distortion of the helical conformation occurs when a CPD contains double T*G wobble pairs (CPD/GG duplex) even though the T residues of the CPD form stable hydrogen bonds with the opposite G residues. The helical bending angle of the CPD/GG duplex was larger than those of the CPD/GA duplex and properly matched CPD/AA duplex. The fluctuation of the backbone conformation and significant changes in the widths of the major and minor grooves at the double T*G wobble paired site were also observed in the CPD/GG duplex. These structural features were also found in a duplex that contains the (6-4) adduct, which is efficiently recognized by the XPC-hHR23B complex. Thus, we suggest that the unique structural features of the DNA double helix (that is, helical bending, flexible backbone conformation, and significant changes of the major and/or minor grooves) might be important factors in determining the binding affinity of the XPC-hHR23B complex to DNA.


===Solution structure of DNA containing CPD opposited by GA===
NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex.,Lee JH, Park CJ, Shin JS, Ikegami T, Akutsu H, Choi BS Nucleic Acids Res. 2004 Apr 30;32(8):2474-81. Print 2004. PMID:15121904<ref>PMID:15121904</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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(as it appears on PubMed at http://www.pubmed.gov), where 15121904 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_15121904}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PIB OCA].
[[Category: Choi BS]]
 
[[Category: Lee JH]]
==Reference==
[[Category: Park CJ]]
NMR structure of the DNA decamer duplex containing double T*G mismatches of cis-syn cyclobutane pyrimidine dimer: implications for DNA damage recognition by the XPC-hHR23B complex., Lee JH, Park CJ, Shin JS, Ikegami T, Akutsu H, Choi BS, Nucleic Acids Res. 2004 Apr 30;32(8):2474-81. Print 2004. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15121904 15121904]
[[Category: Shin JS]]
[[Category: Choi, B S.]]
[[Category: Lee, J H.]]
[[Category: Park, C J.]]
[[Category: Shin, J S.]]
[[Category: Cis-syn cyclobutane pyrimidine dimer]]
[[Category: Cpd containing dna]]
[[Category: Helical distortion]]
[[Category: Thyminedimer]]
 
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