This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1l7t

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:07, 3 April 2024) (edit) (undo)
 
(14 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1l7t.gif|left|200px]]<br /><applet load="1l7t" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1l7t, resolution 2.1&Aring;" />
 
-
'''Crystal Structure Analysis of the anti-testosterone Fab fragment'''<br />
 
-
==Overview==
+
==Crystal Structure Analysis of the anti-testosterone Fab fragment==
-
A highly selective, high affinity recombinant anti-testosterone Fab fragment has been generated by stepwise optimization of the complementarity-determining regions (CDRs) by random mutagenesis and phage display selection of a monoclonal antibody (3-C(4)F(5)). The best mutant (77 Fab) was obtained by evaluating the additivity effects of different independently selected CDR mutations. The 77 Fab contains 20 mutations and has about 40-fold increased affinity (K(d) = 3 x 10(-10) m) when compared with the wild-type (3-C(4)F(5)) Fab. To obtain structural insight into factors, which are needed to improve binding properties, we have determined the crystal structures of the mutant 77 Fab fragment with (2.15 A) and without testosterone (2.10 A) and compared these with previously determined wild-type structures. The overall testosterone binding of the 77 Fab is similar to that of the wild-type. The improved affinity and specificity of the 77 Fab fragment are due to more comprehensive packing of the testosterone with the protein, which is the result of small structural changes within the variable domains. Only one important binding site residue Glu-95 of the heavy chain CDR3 is mutated to alanine in the 77 Fab fragment. This mutation, originally selected from the phage library based on improved specificity, provides more free space for the testosterone D-ring. The light chain CDR1 of 77 Fab containing eight mutations has the most significant effect on the improved affinity, although it has no direct contact with the testosterone. The mutations of CDR-L1 cause a rearrangement in its conformation, leading to an overall fine reshaping of the binding site.
+
<StructureSection load='1l7t' size='340' side='right'caption='[[1l7t]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<table><tr><td colspan='2'>[[1l7t]] 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=1L7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L7T FirstGlance]. <br>
-
1L7T is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] 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=1L7T OCA].
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#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=1l7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l7t OCA], [https://pdbe.org/1l7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l7t RCSB], [https://www.ebi.ac.uk/pdbsum/1l7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l7t ProSAT]</span></td></tr>
-
==Reference==
+
</table>
-
Crystal structure of an in vitro affinity- and specificity-matured anti-testosterone Fab in complex with testosterone. Improved affinity results from small structural changes within the variable domains., Valjakka J, Hemminki A, Niemi S, Soderlund H, Takkinen K, Rouvinen J, J Biol Chem. 2002 Nov 15;277(46):44021-7. Epub 2002 Aug 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12196551 12196551]
+
== Function ==
 +
[https://www.uniprot.org/uniprot/Q91Z05_MOUSE Q91Z05_MOUSE]
 +
== 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/l7/1l7t_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=1l7t ConSurf].
 +
<div style="clear:both"></div>
 +
__TOC__
 +
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
-
[[Category: Protein complex]]
+
[[Category: Hemminki A]]
-
[[Category: Hemminki, A.]]
+
[[Category: Niemi S]]
-
[[Category: Niemi, S.]]
+
[[Category: Rouvinen J]]
-
[[Category: Rouvinen, J.]]
+
[[Category: Soderlund H]]
-
[[Category: Soderlund, H.]]
+
[[Category: Takkinen K]]
-
[[Category: Takkinen, K.]]
+
[[Category: Valjakka J]]
-
[[Category: Valjakka, J.]]
+
-
[[Category: affinity and specificity matured]]
+
-
[[Category: anti-testosterone]]
+
-
[[Category: fab fragment]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:42:20 2008''
+

Current revision

Crystal Structure Analysis of the anti-testosterone Fab fragment

PDB ID 1l7t

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1l7t"
Personal tools