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.


3rdx

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:20, 14 March 2024) (edit) (undo)
 
(5 intermediate revisions not shown.)
Line 1: Line 1:
 +
==Crystal structure of ligand-free R7-2 streptavidin==
==Crystal structure of ligand-free R7-2 streptavidin==
-
<StructureSection load='3rdx' size='340' side='right' caption='[[3rdx]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+
<StructureSection load='3rdx' size='340' side='right'caption='[[3rdx]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[3rdx]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Streptomyces_avidinii Streptomyces avidinii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RDX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RDX FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[3rdx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptomyces_avidinii Streptomyces avidinii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RDX FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</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]] 2.101&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3rdm|3rdm]], [[3rdo|3rdo]], [[3rdq|3rdq]], [[3rds|3rds]], [[3rdu|3rdu]], [[3re5|3re5]], [[3re6|3re6]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=3rdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rdx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rdx RCSB], [http://www.ebi.ac.uk/pdbsum/3rdx PDBsum]</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=3rdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rdx OCA], [https://pdbe.org/3rdx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rdx RCSB], [https://www.ebi.ac.uk/pdbsum/3rdx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rdx ProSAT]</span></td></tr>
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/SAV_STRAV SAV_STRAV] The biological function of streptavidin is not known. Forms a strong non-covalent specific complex with biotin (one molecule of biotin per subunit of streptavidin).
-
We have performed a detailed analysis of streptavidin variants with altered specificity towards desthiobiotin. In addition to changes in key residues which widen the ligand binding pocket and accommodate the more structurally flexible desthiobiotin, the data revealed the role of a key, non-active site mutation at the base of the flexible loop (S52G) which slows dissociation of this ligand by approximately sevenfold. Our data suggest that this mutation results in the loss of a stabilizing contact which keeps this loop open and accessible in the absence of ligand. When this mutation was introduced into the wild-type protein, destabilization of the opened loop conferred a approximately 10-fold decrease in both the on-rate and off-rate for the ligand biotin-4-fluoroscein. A similar effect was observed when this mutation was added to a monomeric form of this protein. Our results provide key insight into the role of the streptavidin flexible loop in ligand binding and maintaining high affinity interactions.
+
-
 
+
-
Evolved streptavidin mutants reveal key role of loop residue in high-affinity binding.,Magalhaes ML, Czekster CM, Guan R, Malashkevich VN, Almo SC, Levy M Protein Sci. 2011 Jul;20(7):1145-54. doi: 10.1002/pro.642. Epub 2011 May, 12. PMID:21520321<ref>PMID:21520321</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
==See Also==
==See Also==
-
*[[Avidin|Avidin]]
+
*[[Avidin 3D structures|Avidin 3D structures]]
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
 +
[[Category: Large Structures]]
[[Category: Streptomyces avidinii]]
[[Category: Streptomyces avidinii]]
-
[[Category: Almo, S C]]
+
[[Category: Almo SC]]
-
[[Category: Czecster, C M]]
+
[[Category: Czecster CM]]
-
[[Category: Guan, R]]
+
[[Category: Guan R]]
-
[[Category: Levy, M]]
+
[[Category: Levy M]]
-
[[Category: Magalhaes, M]]
+
[[Category: Magalhaes M]]
-
[[Category: Malashkevich, V N]]
+
[[Category: Malashkevich VN]]
-
[[Category: Biotin binding protein]]
+
-
[[Category: Improved desthiobiotin binding]]
+
-
[[Category: Opened loop destabilization]]
+
-
[[Category: Streptavidin variant]]
+

Current revision

Crystal structure of ligand-free R7-2 streptavidin

PDB ID 3rdx

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/3rdx"
Personal tools