1shm

From Proteopedia

(Difference between revisions)

Current revision

Convergent solutions to VHH domain stabilization from natural and in vitro evolution

Structural highlights

1shm is a 4 chain structure with sequence from Lama glama. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.9Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The diversity of natural antibodies is limited by the genetic mechanisms that engender diversity and the functional requirements of antigen binding. Using an in vitro-evolved autonomous heavy chain variable domain (V(H)H-RIG), we have investigated the limits of structurally-tolerated diversity in the three complementarity-determining regions and a fourth loop within the third framework region. We determined the X-ray crystal structure of the V(H)H-RIG domain at 1.9A resolution and used it to guide the design of phage-displayed libraries encompassing the four loops. The libraries were subjected to selections for structural stability, and a database of structurally-tolerated sequences was compiled from the sequences of approximately 1000 unique clones. The results reveal that all four loops accommodate significantly greater diversity than is observed in nature. Thus, it appears that most sequence biases in the natural immune repertoire arise from factors other than structural constraints and, consequently, it should be possible to enhance the functions of antibodies significantly through in vitro evolution.

A structure-based database of antibody variable domain diversity.,Bond CJ, Wiesmann C, Marsters JC Jr, Sidhu SS J Mol Biol. 2005 May 6;348(3):699-709. PMID:15826665^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Bond CJ, Wiesmann C, Marsters JC Jr, Sidhu SS. A structure-based database of antibody variable domain diversity. J Mol Biol. 2005 May 6;348(3):699-709. PMID:15826665 doi:10.1016/j.jmb.2005.02.063

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1shm"

@@ Line 1: / Line 1: @@
 ==Convergent solutions to VHH domain stabilization from natural and in vitro evolution==
-<StructureSection load='1shm' size='340' side='right' caption='[[1shm]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='1shm' size='340' side='right'caption='[[1shm]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1shm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Camelus_glama Camelus glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SHM OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1SHM FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1shm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SHM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SHM FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1hcv|1hcv]], [[1mel|1mel]], [[1f2x|1f2x]]</td></tr>
+</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1shm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1shm OCA], [http://pdbe.org/1shm PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1shm RCSB], [http://www.ebi.ac.uk/pdbsum/1shm PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1shm ProSAT]</span></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=1shm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1shm OCA], [https://pdbe.org/1shm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1shm RCSB], [https://www.ebi.ac.uk/pdbsum/1shm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1shm ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 12: / Line 12: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/sh/1shm_consurf.spt"</scriptWhenChecked>
-    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 29: / Line 29: @@
 ==See Also==
 *[[Antibody 3D structures|Antibody 3D structures]]
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Camelus glama]]
+[[Category: Lama glama]]
-[[Category: Bond, C J]]
+[[Category: Large Structures]]
-[[Category: Marsters, J C]]
+[[Category: Bond CJ]]
-[[Category: Sidhu, S S]]
+[[Category: Marsters JC]]
-[[Category: Wiesmann, C]]
+[[Category: Sidhu SS]]
-[[Category: Heavy chain variable domain]]
+[[Category: Wiesmann C]]
-[[Category: Immune system]]
-[[Category: Immunoglobulin]]
-[[Category: Vhh domain]]

1shm

From Proteopedia

Current revision

Convergent solutions to VHH domain stabilization from natural and in vitro evolution

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

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Proteopedia Page Contributors and Editors (what is this?)

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