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| | ==BACTERIOPHAGE LAMBDA HEAD PROTEIN D== | | ==BACTERIOPHAGE LAMBDA HEAD PROTEIN D== |
| - | <StructureSection load='1c5e' size='340' side='right' caption='[[1c5e]], [[Resolution|resolution]] 1.10Å' scene=''> | + | <StructureSection load='1c5e' size='340' side='right'caption='[[1c5e]], [[Resolution|resolution]] 1.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1c5e]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacteriophage_lambda Bacteriophage lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C5E OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1C5E FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1c5e]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Lambda Escherichia virus Lambda]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1C5E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1C5E 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]] 1.1Å</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=1c5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c5e OCA], [http://pdbe.org/1c5e PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1c5e RCSB], [http://www.ebi.ac.uk/pdbsum/1c5e PDBsum]</span></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'>[https://proteopedia.org/fgij/fg.htm?mol=1c5e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1c5e OCA], [https://pdbe.org/1c5e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1c5e RCSB], [https://www.ebi.ac.uk/pdbsum/1c5e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1c5e ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/VCAD_LAMBD VCAD_LAMBD]] Stabilizes the head shell following the rearrangement of the gpE subunits of the head shell lattice that accompanies expansion of the head. There are approximately 420 copies of protein D per mature phage. | + | [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> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c5/1c5e_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/c5/1c5e_consurf.spt"</scriptWhenChecked> |
| | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Bacteriophage lambda]] | + | [[Category: Escherichia virus Lambda]] |
| - | [[Category: Dauter, Z]] | + | [[Category: Large Structures]] |
| - | [[Category: Forrer, P]] | + | [[Category: Dauter Z]] |
| - | [[Category: Pluckthun, A]] | + | [[Category: Forrer P]] |
| - | [[Category: Wlodawer, A]] | + | [[Category: Pluckthun A]] |
| - | [[Category: Yang, F]] | + | [[Category: Wlodawer A]] |
| - | [[Category: Head protein d]]
| + | [[Category: Yang F]] |
| - | [[Category: Phage display]]
| + | |
| - | [[Category: Protein crystal structure]]
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| - | [[Category: Viral protein]]
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| - | [[Category: Virus assembly]]
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| 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]
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 crystal structure of gpD, the capsid-stabilizing protein of bacteriophage lambda, was solved at 1.1 A resolution. Data were obtained from twinned crystals in space group P21 and refined with anisotropic temperature factors to an R-factor of 0.098 (Rfree = 0. 132). GpD (109 residues) has a novel fold with an unusually low content of regular secondary structure. Noncrystallographic trimers with substantial intersubunit interfaces were observed. The C-termini are well ordered and located on one side of the trimer, relatively far from its three-fold axis. The N-termini are disordered up to Ser 15, which is close to the three-fold axis and on the same side as the C-termini. A density map of the icosahedral viral capsid at 15 A resolution, obtained by cryo-electron microscopy and image reconstruction, reveals gpD trimers, seemingly indistinguishable from the ones seen in the crystals, at all three-fold sites. The map further reveals that the side of the trimer that binds to the capsid is the side on which both termini reside. Despite this orientation of the gpD trimer, fusion proteins connected by linker peptides to either terminus bind to the capsid, allowing protein and peptide display.
Novel fold and capsid-binding properties of the lambda-phage display platform protein gpD.,Yang F, Forrer P, Dauter Z, Conway JF, Cheng N, Cerritelli ME, Steven AC, Pluckthun A, Wlodawer A Nat Struct Biol. 2000 Mar;7(3):230-7. PMID:10700283[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
- ↑ Yang F, Forrer P, Dauter Z, Conway JF, Cheng N, Cerritelli ME, Steven AC, Pluckthun A, Wlodawer A. Novel fold and capsid-binding properties of the lambda-phage display platform protein gpD. Nat Struct Biol. 2000 Mar;7(3):230-7. PMID:10700283 doi:10.1038/73347
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