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| | <StructureSection load='2w4z' size='340' side='right'caption='[[2w4z]], [[Resolution|resolution]] 3.60Å' scene=''> | | <StructureSection load='2w4z' size='340' side='right'caption='[[2w4z]], [[Resolution|resolution]] 3.60Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2w4z]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Unclassified_levivirus Unclassified levivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W4Z FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2w4z]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Unclassified_Emesvirus Unclassified Emesvirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2W4Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2W4Z FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <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]] 3.6Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2w4y|2w4y]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <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=2w4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w4z OCA], [https://pdbe.org/2w4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w4z RCSB], [https://www.ebi.ac.uk/pdbsum/2w4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w4z 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=2w4z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2w4z OCA], [https://pdbe.org/2w4z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2w4z RCSB], [https://www.ebi.ac.uk/pdbsum/2w4z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2w4z ProSAT]</span></td></tr> |
| | </table> | | </table> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Unclassified levivirus]] | + | [[Category: Unclassified Emesvirus]] |
| - | [[Category: Dishlers, A]] | + | [[Category: Dishlers A]] |
| - | [[Category: Kazaks, A]] | + | [[Category: Kazaks A]] |
| - | [[Category: Liljas, L]] | + | [[Category: Liljas L]] |
| - | [[Category: Plevka, P]] | + | [[Category: Plevka P]] |
| - | [[Category: Tars, K]] | + | [[Category: Tars K]] |
| - | [[Category: Assembly]]
| + | |
| - | [[Category: Calcium ion]]
| + | |
| - | [[Category: Rna]]
| + | |
| - | [[Category: Virus]]
| + | |
| Structural highlights
Publication Abstract from PubMed
The structure of the Leviviridae bacteriophage phiCb5 virus-like particle has been determined at 2.9 A resolution and the structure of the native bacteriophage phiCb5 at 3.6 A. The structures of the coat protein shell appear to be identical, while differences are found in the organization of the density corresponding to the RNA. The capsid is built of coat protein dimers and in shape corresponds to a truncated icosahedron with T = 3 quasi-symmetry. The capsid is stabilized by four calcium ions per icosahedral asymmetric unit. One is located at the symmetry axis relating the quasi-3-fold related subunits and is part of an elaborate network of hydrogen bonds stabilizing the interface. The remaining calcium ions stabilize the contacts within the coat protein dimer. The stability of the phiCb5 particles decreases when calcium ions are chelated with EDTA. In contrast to other leviviruses, phiCb5 particles are destabilized in solution with elevated salt concentration. The model of the phiCb5 capsid provides an explanation of the salt-induced destabilization of phiCb5, since hydrogen bonds, salt bridges and calcium ions have important roles in the intersubunit interactions. Electron density of three putative RNA nucleotides per icosahedral asymmetric unit has been observed in the phiCb5 structure. The nucleotides mediate contacts between the two subunits forming a dimer and a third subunit in another dimer. We suggest a model for phiCb5 capsid assembly in which addition of coat protein dimers to the forming capsid is facilitated by interaction with the RNA genome. The phiCb5 structure is the first example in the levivirus family that provides insight into the mechanism by which the genome-coat protein interaction may accelerate the capsid assembly and increase capsid stability.
The structure of bacteriophage phiCb5 reveals a role of the RNA genome and metal ions in particle stability and assembly.,Plevka P, Kazaks A, Voronkova T, Kotelovica S, Dishlers A, Liljas L, Tars K J Mol Biol. 2009 Aug 21;391(3):635-47. Epub 2009 Jun 23. PMID:19559027[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Plevka P, Kazaks A, Voronkova T, Kotelovica S, Dishlers A, Liljas L, Tars K. The structure of bacteriophage phiCb5 reveals a role of the RNA genome and metal ions in particle stability and assembly. J Mol Biol. 2009 Aug 21;391(3):635-47. Epub 2009 Jun 23. PMID:19559027 doi:10.1016/j.jmb.2009.06.047
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