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| | ==Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5== | | ==Designed armadillo repeat protein YIIIM''6AII in complex with pD_(KR)5== |
| - | <StructureSection load='5mfd' size='340' side='right' caption='[[5mfd]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='5mfd' size='340' side='right'caption='[[5mfd]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5mfd]] is a 12 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MFD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5MFD FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5mfd]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5MFD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5MFD FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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]] 2.3Å</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=5mfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mfd OCA], [http://pdbe.org/5mfd PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mfd RCSB], [http://www.ebi.ac.uk/pdbsum/5mfd PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mfd ProSAT]</span></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</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=5mfd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mfd OCA], [https://pdbe.org/5mfd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5mfd RCSB], [https://www.ebi.ac.uk/pdbsum/5mfd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5mfd ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/DECO_LAMBD DECO_LAMBD]] Stabilizes the expansion of the capsid head shell after genome packaging. The packaging of viral genome in the procapsid triggers a dramatic reconfiguration of the capsid shell, expanding from roughly 50nm to 60nm while the capsid thickness decreases. 415 capsid decoration protein molecules cooperatively bind the expanded capsid, thereby stabilizing the mature capsid shell.<ref>PMID:18786402</ref> <ref>PMID:21821043</ref> <ref>PMID:8411174</ref> | + | [https://www.uniprot.org/uniprot/DECO_LAMBD DECO_LAMBD] Stabilizes the expansion of the capsid head shell after genome packaging. The packaging of viral genome in the procapsid triggers a dramatic reconfiguration of the capsid shell, expanding from roughly 50nm to 60nm while the capsid thickness decreases. 415 capsid decoration protein molecules cooperatively bind the expanded capsid, thereby stabilizing the mature capsid shell.<ref>PMID:18786402</ref> <ref>PMID:21821043</ref> <ref>PMID:8411174</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Hansen, S]] | + | [[Category: Escherichia virus Lambda]] |
| - | [[Category: Kiefer, J]] | + | [[Category: Large Structures]] |
| - | [[Category: Madhurantakam, C]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Mittl, P]] | + | [[Category: Hansen S]] |
| - | [[Category: Plueckthun, A]] | + | [[Category: Kiefer J]] |
| - | [[Category: De novo protein]] | + | [[Category: Madhurantakam C]] |
| - | [[Category: Designed armadillo repeat protein]] | + | [[Category: Mittl P]] |
| - | [[Category: Peptide binding]] | + | [[Category: Plueckthun A]] |
| Structural highlights
Function
DECO_LAMBD Stabilizes the expansion of the capsid head shell after genome packaging. The packaging of viral genome in the procapsid triggers a dramatic reconfiguration of the capsid shell, expanding from roughly 50nm to 60nm while the capsid thickness decreases. 415 capsid decoration protein molecules cooperatively bind the expanded capsid, thereby stabilizing the mature capsid shell.[1] [2] [3]
Publication Abstract from PubMed
Designed armadillo repeat proteins (dArmRP) are alpha-helical solenoid repeat proteins with an extended peptide binding groove that were engineered to develop a generic modular technology for peptide recognition. In this context, the term "peptide" not only denotes a short unstructured chain of amino acids, but also an unstructured region of a protein, as they occur in termini, loops, or linkers between folded domains. Here we report two crystal structures of dArmRPs, in complex with peptides fused either to the N-terminus of Green Fluorescent Protein or to the C-terminus of a phage lambda protein D. These structures demonstrate that dArmRPs bind unfolded peptides in the intended conformation also when they constitute unstructured parts of folded proteins, which greatly expands possible applications of the dArmRP technology. Nonetheless, the structures do not fully reflect the binding behavior in solution, that is, some binding sites remain unoccupied in the crystal and even unexpected peptide residues appear to be bound. We show how these differences can be explained by restrictions of the crystal lattice or the composition of the crystallization solution. This illustrates that crystal structures have to be interpreted with caution when protein-peptide interactions are characterized, and should always be correlated with measurements in solution.
Structures of designed armadillo repeat proteins binding to peptides fused to globular domains.,Hansen S, Kiefer JD, Madhurantakam C, Mittl PRE, Pluckthun A Protein Sci. 2017 Oct;26(10):1942-1952. doi: 10.1002/pro.3229. Epub 2017 Jul 25. PMID:28691351[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Lander GC, Evilevitch A, Jeembaeva M, Potter CS, Carragher B, Johnson JE. Bacteriophage lambda stabilization by auxiliary protein gpD: timing, location, and mechanism of attachment determined by cryo-EM. Structure. 2008 Sep 10;16(9):1399-406. doi: 10.1016/j.str.2008.05.016. PMID:18786402 doi:http://dx.doi.org/10.1016/j.str.2008.05.016
- ↑ Medina EM, Andrews BT, Nakatani E, Catalano CE. The bacteriophage lambda gpNu3 scaffolding protein is an intrinsically disordered and biologically functional procapsid assembly catalyst. J Mol Biol. 2011 Sep 30;412(4):723-36. doi: 10.1016/j.jmb.2011.07.045. Epub 2011 , Jul 29. PMID:21821043 doi:http://dx.doi.org/10.1016/j.jmb.2011.07.045
- ↑ Dokland T, Murialdo H. Structural transitions during maturation of bacteriophage lambda capsids. J Mol Biol. 1993 Oct 20;233(4):682-94. PMID:8411174 doi:http://dx.doi.org/10.1006/jmbi.1993.1545
- ↑ Hansen S, Kiefer JD, Madhurantakam C, Mittl PRE, Pluckthun A. Structures of designed armadillo repeat proteins binding to peptides fused to globular domains. Protein Sci. 2017 Oct;26(10):1942-1952. doi: 10.1002/pro.3229. Epub 2017 Jul 25. PMID:28691351 doi:http://dx.doi.org/10.1002/pro.3229
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