3eot: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,328,572 edits
No edit summary
 
(10 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{Seed}}
[[Image:3eot.jpg|left|200px]]


<!--
==Crystal structure of LAC031, an engineered anti-VLA1 Fab==
The line below this paragraph, containing "STRUCTURE_3eot", creates the "Structure Box" on the page.
<StructureSection load='3eot' size='340' side='right'caption='[[3eot]], [[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'>[[3eot]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EOT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3EOT 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3eot FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3eot OCA], [https://pdbe.org/3eot PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3eot RCSB], [https://www.ebi.ac.uk/pdbsum/3eot PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3eot ProSAT]</span></td></tr>
{{STRUCTURE_3eot|  PDB=3eot  |  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/eo/3eot_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=3eot ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
A design approach was taken to investigate the feasibility of replacing single complementarity determining region (CDR) antibody loops. This approach may complement simpler mutation-based strategies for rational antibody design by expanding conformation space. Enormous crystal structure diversity is available, making CDR loops logical targets for structure-based design. A detailed analysis for the L1 loop shows that each loop length takes a distinct conformation, thereby allowing control on a length scale beyond that accessible to simple mutations. The L1 loop in the anti-VLA1 antibody was replaced with the L2 loop residues longer in an attempt to add an additional hydrogen bond and fill space on the antibody-antigen interface. The designs expressed well, but failed to improve affinity. In an effort to learn more, one design was crystallized and data were collected at 1.9 A resolution. The designed L1 loop takes the qualitatively desired conformation; confirming that loop replacement by design is feasible. The crystal structure also shows that the outermost loop (residues Leu51-Ser68) is domain swapped with another monomer. Tryptophan fluorescence measurements were used to monitor unfolding as a function of temperature and indicate that the loop involved in domain swapping does not unfold below 60 degrees C. The domain-swapping is not directly responsible for the affinity loss, but is likely a side-effect of the structural instability which may contribute to affinity loss. A second round of design was successful in eliminating the dimerization through mutation of a residue (Leu51Ser) at the joint of the domain-swapped loop.


===Crystal structure of LAC031, an engineered anti-VLA1 Fab===
An antibody loop replacement design feasibility study and a loop-swapped dimer structure.,Clark LA, Boriack-Sjodin PA, Day E, Eldredge J, Fitch C, Jarpe M, Miller S, Li Y, Simon K, van Vlijmen HW Protein Eng Des Sel. 2009 Feb;22(2):93-101. Epub 2008 Dec 10. PMID:19074157<ref>PMID:19074157</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3eot" style="background-color:#fffaf0;"></div>


<!--
==See Also==
The line below this paragraph, {{ABSTRACT_PUBMED_19074157}}, adds the Publication Abstract to the page
*[[Antibody 3D structures|Antibody 3D structures]]
(as it appears on PubMed at http://www.pubmed.gov), where 19074157 is the PubMed ID number.
*[[Sandbox 20009|Sandbox 20009]]
-->
*[[3D structures of non-human antibody|3D structures of non-human antibody]]
{{ABSTRACT_PUBMED_19074157}}
== References ==
 
<references/>
==About this Structure==
__TOC__
3EOT is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3EOT OCA].
</StructureSection>
 
[[Category: Large Structures]]
==Reference==
<ref group="xtra">PMID:19074157</ref><references group="xtra"/>
[[Category: Mus musculus]]
[[Category: Mus musculus]]
[[Category: Boriack-Sjodin, P A.]]
[[Category: Boriack-Sjodin PA]]
[[Category: Clark, L A.]]
[[Category: Clark LA]]
[[Category: Antibody]]
[[Category: Domain swap]]
[[Category: Fab]]
[[Category: Immune system]]
[[Category: Proten engineering]]
[[Category: Vla-1]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 21 10:46:48 2009''
Retrieved from "https://proteopedia.org/3eot"