2r2v: Difference between revisions

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-{{Seed}}
-[[Image:2r2v.png|left|200px]]
-<!--
+==Sequence Determinants of the Topology of the Lac Repressor Tetrameric Coiled Coil==
-The line below this paragraph, containing "STRUCTURE_2r2v", creates the "Structure Box" on the page.
+<StructureSection load='2r2v' size='340' side='right'caption='[[2r2v]], [[Resolution|resolution]] 1.90&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'>[[2r2v]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R2V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2R2V 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]] 1.9&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CIT:CITRIC+ACID'>CIT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_2r2v|  PDB=2r2v  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2r2v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2r2v OCA], [https://pdbe.org/2r2v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2r2v RCSB], [https://www.ebi.ac.uk/pdbsum/2r2v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2r2v ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Predictive understanding of how the folded, functional shape of a native protein is encoded in the linear sequence of its amino acid residues remains an unsolved challenge in modern structural biology. Antiparallel four-stranded coiled coils are relatively simple protein structures that embody a heptad sequence repeat and rich diversity for tertiary packing of alpha-helices. To explore specific sequence determinants of the lac repressor coiled-coil tetramerization domain, we have engineered a set of buried nonpolar side chains at the a-, d-, and e-positions into the hydrophobic interior of the dimeric GCN4 leucine zipper. Circular dichroism and equilibrium ultracentrifugation studies show that this core variant (GCN4-pAeLV) forms a stable tetrameric structure with a reversible and highly cooperative thermal unfolding transition. The X-ray crystal structure at 1.9 A reveals that GCN4-pAeLV is an antiparallel four-stranded coiled coil of the lac repressor type in which the a, d, and e side chains associate by means of combined knobs-against-knobs and knobs-into-holes packing with a characteristic interhelical offset of 0.25 heptad. Comparison of the side chain shape and packing in the antiparallel tetramers shows that the burial of alanine residues at the e positions between the neighboring helices of GCN4-pAeLV dictates both the antiparallel orientation and helix offset. This study fills in a gap in our knowledge of the determinants of structural specificity in antiparallel coiled coils and improves our understanding of how specific side chain packing forms the teritiary structure of a functional protein.
-===Sequence Determinants of the Topology of the Lac Repressor Tetrameric Coiled Coil===
+Conformational specificity of the lac repressor coiled-coil tetramerization domain.,Liu J, Zheng Q, Deng Y, Li Q, Kallenbach NR, Lu M Biochemistry. 2007 Dec 25;46(51):14951-9. Epub 2007 Dec 4. PMID:18052214<ref>PMID:18052214</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2r2v" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18052214}}, adds the Publication Abstract to the page
+*[[Gcn4 3D Structures|Gcn4 3D Structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18052214 is the PubMed ID number.
+*[[Gnc4 3D Structures|Gnc4 3D Structures]]
--->
+*[[Lac repressor|Lac repressor]]
-{{ABSTRACT_PUBMED_18052214}}
+== References ==
+<references/>
-==About this Structure==
+__TOC__
-R2V is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2R2V OCA].
+</StructureSection>
+[[Category: Large Structures]]
-==Reference==
-Conformational specificity of the lac repressor coiled-coil tetramerization domain., Liu J, Zheng Q, Deng Y, Li Q, Kallenbach NR, Lu M, Biochemistry. 2007 Dec 25;46(51):14951-9. Epub 2007 Dec 4. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18052214 18052214]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Liu J]]
-[[Category: Liu, J.]]
+[[Category: Lu M]]
-[[Category: Lu, M.]]
-[[Category: Anti-parallel tetramer]]
-[[Category: Coiled coil]]
-[[Category: De novo protein]]
-[[Category: Protein design]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 02:48:40 2008''