1yyx: Difference between revisions

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


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==The solution structure of a redesigned apocytochrome B562 (Rd-apocyt b562) at 2.8M urea==
The line below this paragraph, containing "STRUCTURE_1yyx", creates the "Structure Box" on the page.
<StructureSection load='1yyx' size='340' side='right'caption='[[1yyx]]' 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'>[[1yyx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YYX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1YYX 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>
-->
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1yyx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1yyx OCA], [https://pdbe.org/1yyx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1yyx RCSB], [https://www.ebi.ac.uk/pdbsum/1yyx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1yyx ProSAT]</span></td></tr>
{{STRUCTURE_1yyx|  PDB=1yyx  |  SCENE=  }}
</table>
== 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/yy/1yyx_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=1yyx ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The absence of detectable kinetic and equilibrium folding intermediates by optical probes is commonly taken to indicate that protein folding is a two-state process. However, for some small proteins with apparent two-state behavior, unfolding intermediates have been identified in native-state hydrogen exchange or kinetic unfolding experiments monitored by nuclear magnetic resonance. Rd-apocytochrome b(562), a four-helix bundle, is one such protein. Here, we found another unfolding intermediate for Rd-apocytochrome b(562). It is based on a cooperative transition of (15)N chemical shifts of amide protons as a function of urea concentrations before the global unfolding. We have solved the high-resolution structure of the protein at 2.8 M urea, which is after this cooperative transition but before the global unfolding. All four helices remained intact, but a number of hydrophobic core residues repacked. This intermediate provides a possible structural interpretation for the kinetic unfolding intermediates observed using nuclear magnetic resonance methods for several proteins and has important implications for theoretical studies of protein folding.


===The solution structure of a redesigned apocytochrome B562 (Rd-apocyt b562) at 2.8M urea===
Detection and structure determination of an equilibrium unfolding intermediate of Rd-apocytochrome b562: native fold with non-native hydrophobic interactions.,Feng H, Vu ND, Bai Y J Mol Biol. 2004 Nov 5;343(5):1477-85. PMID:15491625<ref>PMID:15491625</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
The line below this paragraph, {{ABSTRACT_PUBMED_15491625}}, adds the Publication Abstract to the page
<div class="pdbe-citations 1yyx" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 15491625 is the PubMed ID number.
== References ==
-->
<references/>
{{ABSTRACT_PUBMED_15491625}}
__TOC__
 
</StructureSection>
==About this Structure==
[[Category: Homo sapiens]]
1YYX is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1YYX OCA].
[[Category: Large Structures]]
 
[[Category: Bai Y]]
==Reference==
[[Category: Feng H]]
<ref group="xtra">PMID:15491625</ref><references group="xtra"/>
[[Category: Vu N]]
[[Category: BSGC, Berkeley Structural Genomics Center.]]
[[Category: Bai, Y.]]
[[Category: Feng, H.]]
[[Category: Vu, N.]]
[[Category: Berkeley structural genomics center]]
[[Category: Bsgc]]
[[Category: Hydrophobic interaction]]
[[Category: Intermediate]]
[[Category: Protein structure initiative]]
[[Category: Psi]]
[[Category: Rd-apocyt b562]]
[[Category: Structural genomic]]
 
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