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1q2t

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[[Image:1q2t.gif|left|200px]]
 
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{{Structure
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==Solution structure of d(5mCCTCTCC)4==
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|PDB= 1q2t |SIZE=350|CAPTION= <scene name='initialview01'>1q2t</scene>
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<StructureSection load='1q2t' size='340' side='right'caption='[[1q2t]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[1q2t]] is a 4 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q2T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q2T FirstGlance]. <br>
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|ACTIVITY=
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</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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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MCY:5-METHYL-2-DEOXYCYTIDINE'>MCY</scene></td></tr>
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}}
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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=1q2t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q2t OCA], [https://pdbe.org/1q2t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q2t RCSB], [https://www.ebi.ac.uk/pdbsum/1q2t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q2t ProSAT]</span></td></tr>
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</table>
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'''Solution structure of d(5mCCTCTCC)4'''
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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==Overview==
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The i-motif is a four-stranded structure built by intercalation in head-to-tail orientation of two parallel duplexes associated by hemi-protonated C.C(+) pairs. Using NMR methods, we investigated the structure, the base-pair opening kinetics and the internal motions of three i-motif tetramers: [d(5mCCTCnTCC)](4) (n=1, 2, 3). These tetramers cannot accommodate the intercalation of two T.T pairs in face-to-face orientation. They are built by intercalation of two symmetrical duplexes whose contacting T3/TM thymidine bases (M=5, 6, 7) are either base-paired or unstacked. The arrangement of the unstacked/paired thymidine bases of the two T/T groups results in the formation of two different conformations. One, fully symmetric, whose thymidine bases T3 and TM are unstacked and base-paired respectively. The other is the asymmetric assembly of two duplexes: one where both thymidine bases are unstacked and the other with two T.T pairs. The proportion of the symmetric conformer increases from a value beyond the detection threshold for n=1, to 19% for n=2 and up to more than 95% for n=3. The exchange cross-peaks connecting together the intercalated duplexes of [d(5mCCTCTCC)](4) and [d(5mCCTCCTCC)](4) reveal a structural interconversion induced by the simultaneous opening/closing of the contacting T3/TM thymidine bases. In [d(5mCCTCCTCC)](4) the motion of the T3/T6 groups triggers the interconversion of the symmetric and asymmetric conformations. In [d(5mCCTCTCC)](4) the intercalated duplexes exchange their structures in an apparently concerted motion, suggesting the simultaneous opening/closing of two distant T3/T5* and T5/T3* switching groups. The spectrum of [d(5mCCTCCCTCC)](4) is fully symmetric and, for this reason, its spectrum gives no indication for duplex interconversion. Nevertheless, the imino proton exchange kinetics argues for a switching motion of the T3/T7 group. Duplex interconversion is not detectable in that case, due to the tetramer symmetry. The origin of the structural conflict hindering the intercalation of two T.T pairs into the i-motif is discussed.
The i-motif is a four-stranded structure built by intercalation in head-to-tail orientation of two parallel duplexes associated by hemi-protonated C.C(+) pairs. Using NMR methods, we investigated the structure, the base-pair opening kinetics and the internal motions of three i-motif tetramers: [d(5mCCTCnTCC)](4) (n=1, 2, 3). These tetramers cannot accommodate the intercalation of two T.T pairs in face-to-face orientation. They are built by intercalation of two symmetrical duplexes whose contacting T3/TM thymidine bases (M=5, 6, 7) are either base-paired or unstacked. The arrangement of the unstacked/paired thymidine bases of the two T/T groups results in the formation of two different conformations. One, fully symmetric, whose thymidine bases T3 and TM are unstacked and base-paired respectively. The other is the asymmetric assembly of two duplexes: one where both thymidine bases are unstacked and the other with two T.T pairs. The proportion of the symmetric conformer increases from a value beyond the detection threshold for n=1, to 19% for n=2 and up to more than 95% for n=3. The exchange cross-peaks connecting together the intercalated duplexes of [d(5mCCTCTCC)](4) and [d(5mCCTCCTCC)](4) reveal a structural interconversion induced by the simultaneous opening/closing of the contacting T3/TM thymidine bases. In [d(5mCCTCCTCC)](4) the motion of the T3/T6 groups triggers the interconversion of the symmetric and asymmetric conformations. In [d(5mCCTCTCC)](4) the intercalated duplexes exchange their structures in an apparently concerted motion, suggesting the simultaneous opening/closing of two distant T3/T5* and T5/T3* switching groups. The spectrum of [d(5mCCTCCCTCC)](4) is fully symmetric and, for this reason, its spectrum gives no indication for duplex interconversion. Nevertheless, the imino proton exchange kinetics argues for a switching motion of the T3/T7 group. Duplex interconversion is not detectable in that case, due to the tetramer symmetry. The origin of the structural conflict hindering the intercalation of two T.T pairs into the i-motif is discussed.
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==About this Structure==
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T.T pair intercalation and duplex interconversion within i-motif tetramers.,Leroy JL J Mol Biol. 2003 Oct 10;333(1):125-39. PMID:14516748<ref>PMID:14516748</ref>
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1Q2T 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=1Q2T OCA].
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==Reference==
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T.T pair intercalation and duplex interconversion within i-motif tetramers., Leroy JL, J Mol Biol. 2003 Oct 10;333(1):125-39. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14516748 14516748]
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[[Category: Protein complex]]
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[[Category: Leroy, J L.]]
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[[Category: dna solution structure; i-motif; protonated cytidine; hemiprotonated base-pair]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:32:16 2008''
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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 1q2t" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Leroy J-L]]

Current revision

Solution structure of d(5mCCTCTCC)4

PDB ID 1q2t

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