3noc

From Proteopedia

(Difference between revisions)

Revision as of 07:06, 12 May 2022

Designed ankyrin repeat protein (DARPin) binders to AcrB: Plasticity of the Interface

Structural highlights

3noc is a 5 chain structure with sequence from Ecoli and Synthetic construct sequences. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
NonStd Res:
Related:	2j8s, 3nog
Gene:	acrB, acrE, b0462, JW0451 (ECOLI)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[ACRB_ECOLI] AcrAB is a drug efflux protein with a broad substrate specificity.^[1] ^[2] ^[3]

Publication Abstract from PubMed

The formation of well-diffracting crystals is a major bottleneck in structural analysis of membrane proteins by X-ray crystallography. One approach to improve crystal quality is the use of DARPins as crystallization chaperones. Here, we present a detailed analysis of the interaction between DARPins and the integral membrane protein AcrB. We find that binders selected in vitro by ribosome display share a common epitope. The comparative analysis of three crystal structures of AcrB-DARPin complexes allowed us to study the plasticity of the interaction with this dominant binding site. Seemingly redundant AcrB-DARPin crystals show substantially different diffraction quality as a result of subtle differences in the binding geometry. This work exemplifies the importance to screen a number of crystallization chaperones to obtain optimal diffraction data. Crystallographic analysis is complemented by biophysical characterization of nine AcrB binders. We observe that small variations in the interface can lead to differing behavior of the DARPins with regards to affinity, stoichiometry of the complexes and specificity for their target.

Designed ankyrin repeat protein binders for the crystallization of AcrB: Plasticity of the dominant interface.,Monroe N, Sennhauser G, Seeger MA, Briand C, Grutter MG J Struct Biol. 2011 May;174(2):269-81. Epub 2011 Feb 4. PMID:21296164^[4]

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

References

↑ Murakami S, Nakashima R, Yamashita E, Matsumoto T, Yamaguchi A. Crystal structures of a multidrug transporter reveal a functionally rotating mechanism. Nature. 2006 Sep 14;443(7108):173-9. Epub 2006 Aug 16. PMID:16915237 doi:10.1038/nature05076
↑ Seeger MA, Schiefner A, Eicher T, Verrey F, Diederichs K, Pos KM. Structural asymmetry of AcrB trimer suggests a peristaltic pump mechanism. Science. 2006 Sep 1;313(5791):1295-8. PMID:16946072 doi:313/5791/1295
↑ Sennhauser G, Amstutz P, Briand C, Storchenegger O, Grutter MG. Drug export pathway of multidrug exporter AcrB revealed by DARPin inhibitors. PLoS Biol. 2007 Jan;5(1):e7. PMID:17194213 doi:10.1371/journal.pbio.0050007
↑ Monroe N, Sennhauser G, Seeger MA, Briand C, Grutter MG. Designed ankyrin repeat protein binders for the crystallization of AcrB: Plasticity of the dominant interface. J Struct Biol. 2011 May;174(2):269-81. Epub 2011 Feb 4. PMID:21296164 doi:10.1016/j.jsb.2011.01.014

1 Structural highlights
2 Function
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/3noc"

@@ Line 1: / Line 1: @@
 ==Designed ankyrin repeat protein (DARPin) binders to AcrB: Plasticity of the Interface==
-<StructureSection load='3noc' size='340' side='right' caption='[[3noc]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='3noc' size='340' side='right'caption='[[3noc]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3noc]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli] and [http://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NOC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3NOC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3noc]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli] and [https://en.wikipedia.org/wiki/Synthetic_construct_sequences Synthetic construct sequences]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NOC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NOC FirstGlance]. <br>
 </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2j8s|2j8s]], [[3nog|3nog]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2j8s|2j8s]], [[3nog|3nog]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">acrB, acrE, b0462, JW0451 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">acrB, acrE, b0462, JW0451 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=3noc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3noc OCA], [http://pdbe.org/3noc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3noc RCSB], [http://www.ebi.ac.uk/pdbsum/3noc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3noc 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=3noc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3noc OCA], [https://pdbe.org/3noc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3noc RCSB], [https://www.ebi.ac.uk/pdbsum/3noc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3noc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ACRB_ECOLI ACRB_ECOLI]] AcrAB is a drug efflux protein with a broad substrate specificity.<ref>PMID:16915237</ref> <ref>PMID:16946072</ref> <ref>PMID:17194213</ref>
+[[https://www.uniprot.org/uniprot/ACRB_ECOLI ACRB_ECOLI]] AcrAB is a drug efflux protein with a broad substrate specificity.<ref>PMID:16915237</ref> <ref>PMID:16946072</ref> <ref>PMID:17194213</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 22: @@
 ==See Also==
-*[[Ankyrin|Ankyrin]]
+*[[Ankyrin 3D structures|Ankyrin 3D structures]]
 == References ==
 <references/>
@@ Line 28: / Line 28: @@
 </StructureSection>
 [[Category: Ecoli]]
+[[Category: Large Structures]]
 [[Category: Synthetic construct sequences]]
 [[Category: Briand, C]]

3noc

From Proteopedia

Revision as of 07:06, 12 May 2022

Designed ankyrin repeat protein (DARPin) binders to AcrB: Plasticity of the Interface

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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