2qyj

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of a designed full consensus ankyrin

Structural highlights

2qyj is a 1 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.05Å
Ligands:
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

Full-consensus designed ankyrin repeat proteins (DARPins), in which randomized positions of the previously described DARPin library have been fixed, are characterized. They show exceptionally high thermodynamic stabilities, even when compared to members of consensus DARPin libraries and even more so when compared to naturally occurring ankyrin repeat proteins. We determined the crystal structure of a full-consensus DARPin, containing an N-capping repeat, three identical internal repeats and a C-capping repeat at 2.05 A resolution, and compared its structure with that of the related DARPin library members E3_5 and E3_19. This structural comparison suggests that primarily salt bridges on the surface, which arrange in a network with almost crystal-like regularity, increase thermostability in the full-consensus NI(3)C DARPin to make it resistant to boiling. In the crystal structure, three sulfate ions complement this network. Thermal denaturation experiments in guanidine hydrochloride directly indicate a contribution of sulfate binding to the stability, providing further evidence for the stabilizing effect of surface-exposed electrostatic interactions and regular charge networks. The charged residues at the place of randomized residues in the DARPin libraries were selected based on sequence statistics and suggested that the charge interaction network is a hidden design feature of this protein family. Ankyrins can therefore use design principles from proteins of thermophilic organisms and reach at least similar stabilities.

Stabilizing ionic interactions in a full-consensus ankyrin repeat protein.,Merz T, Wetzel SK, Firbank S, Pluckthun A, Grutter MG, Mittl PR J Mol Biol. 2008 Feb 8;376(1):232-40. Epub 2007 Nov 22. PMID:18155045^[1]

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

References

↑ Merz T, Wetzel SK, Firbank S, Pluckthun A, Grutter MG, Mittl PR. Stabilizing ionic interactions in a full-consensus ankyrin repeat protein. J Mol Biol. 2008 Feb 8;376(1):232-40. Epub 2007 Nov 22. PMID:18155045 doi:10.1016/j.jmb.2007.11.047

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/2qyj"

Categories: Large Structures | Merz T | Z-disk

@@ Line 1: / Line 1: @@
 ==Crystal structure of a designed full consensus ankyrin==
-<StructureSection load='2qyj' size='340' side='right' caption='[[2qyj]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
+<StructureSection load='2qyj' size='340' side='right'caption='[[2qyj]], [[Resolution|resolution]] 2.05&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qyj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QYJ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2QYJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2qyj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QYJ FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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]] 2.05&#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=2qyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qyj OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2qyj RCSB], [http://www.ebi.ac.uk/pdbsum/2qyj PDBsum]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=2qyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qyj OCA], [https://pdbe.org/2qyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qyj RCSB], [https://www.ebi.ac.uk/pdbsum/2qyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qyj ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 10: / Line 12: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qy/2qyj_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qy/2qyj_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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2qyj ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 24: / Line 26: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2qyj" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Ankyrin|Ankyrin]]
+*[[Ankyrin 3D structures|Ankyrin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Merz, T]]
+[[Category: Large Structures]]
-[[Category: Ankyrin repeat]]
+[[Category: Merz T]]
-[[Category: De novo protein]]
+[[Category: Z-disk]]
-[[Category: Helix-turn-helix-beta-turn]]
-[[Category: Repeat protein]]

2qyj

From Proteopedia

Current revision

Crystal structure of a designed full consensus ankyrin

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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