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1rb8

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[[Image:1rb8.gif|left|200px]]<br /><applet load="1rb8" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1rb8, resolution 3.50&Aring;" />
 
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'''The phiX174 DNA binding protein J in two different capsid environments.'''<br />
 
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==Overview==
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==The phiX174 DNA binding protein J in two different capsid environments.==
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Packaging of viral genomes into their respective capsids requires partial neutralization of the highly negatively charged RNA or DNA. Many viruses, including the Microviridae bacteriophages phiX174, G4, and alpha3, have solved this problem by coding for a highly positively charged nucleic acid-binding protein that is packaged along with the genome. The phiX174 DNA-binding protein, J, is 13 amino acid residues longer than the alpha3 and G4 J proteins by virtue of an additional nucleic acid-binding domain at the amino terminus. Chimeric phiX174 particles containing the smaller DNA-binding protein cannot be generated due to procapsid instability during DNA packaging. However, chimeric alpha3 and G4 phages, containing the phiX174 DNA-binding protein in place of the endogenous J protein, assemble and are infectious, but are less dense than the respective wild-type species. In addition, host cell attachment and native gel migration assays indicate surface variations of these viruses that are controlled by the nature of the J protein. The structure of alpha3 packaged with phiX174 J protein was determined to 3.5A resolution and compared with the previously determined structures of phiX174 and alpha3. The structures of the capsid and spike proteins in the chimeric particle remain unchanged within experimental error when compared to the wild-type alpha3 virion proteins. The amino-terminal region of the phiX174 J protein, which is missing from wild-type alpha3 virions, is mostly disordered in the alpha3 chimera. The differences observed between solution properties of wild-type phiX174, wild-type alpha3, and alpha3 chimera, including their ability to attach to host cells, correlates with the degree of order in the amino-terminal domain of the J protein. When ordered, this domain binds to the interior of the viral capsid and, thus, might control the flexibility of the capsid. In addition, the properties of the phiX174 J protein in the chimera and the results of mutational analyses suggest that an evolutionary correlation may exist between the size of the J protein and the stoichiometry of the DNA pilot protein H, required in the initial stages of infection. Hence, the function of the J protein is to facilitate DNA packaging, as well as to mediate surface properties such as cell attachment and infection.
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<StructureSection load='1rb8' size='340' side='right'caption='[[1rb8]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1rb8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_alpha3 Escherichia phage alpha3] and [https://en.wikipedia.org/wiki/Escherichia_virus_phiX174 Escherichia virus phiX174]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RB8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RB8 FirstGlance]. <br>
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1RB8 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_alpha3 Enterobacteria phage alpha3] and [http://en.wikipedia.org/wiki/Enterobacteria_phage_phix174 Enterobacteria phage phix174] with <scene name='pdbligand=C:'>C</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RB8 OCA].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.5&#8491;</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rb8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rb8 OCA], [https://pdbe.org/1rb8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rb8 RCSB], [https://www.ebi.ac.uk/pdbsum/1rb8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rb8 ProSAT]</span></td></tr>
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==Reference==
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</table>
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The phiX174 protein J mediates DNA packaging and viral attachment to host cells., Bernal RA, Hafenstein S, Esmeralda R, Fane BA, Rossmann MG, J Mol Biol. 2004 Apr 9;337(5):1109-22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15046981 15046981]
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== Function ==
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[[Category: Enterobacteria phage alpha3]]
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[https://www.uniprot.org/uniprot/CAPSD_BPAL3 CAPSD_BPAL3] Assembles to form an icosahedral capsid with a T=1 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins F. Upon virus binding to host cell, one of the spikes dissociates from the capsid and the virus interacts with LPS through the exposed EF loops on the F proteins. After the genome had been ejected, the channel formed by the F proteins at the unique fivefold axis remains open.[UniProtKB:P03641]
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[[Category: Enterobacteria phage phix174]]
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== Evolutionary Conservation ==
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[[Category: Protein complex]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Bernal, R A.]]
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Check<jmol>
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[[Category: Esmeralda, R.]]
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<jmolCheckbox>
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[[Category: Fane, B A.]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rb/1rb8_consurf.spt"</scriptWhenChecked>
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[[Category: Hafenstein, S.]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: Rossmann, M G.]]
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<text>to colour the structure by Evolutionary Conservation</text>
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[[Category: C]]
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</jmolCheckbox>
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[[Category: alpha3]]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1rb8 ConSurf].
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[[Category: bacteriophage alpha3]]
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<div style="clear:both"></div>
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[[Category: bacteriophage alpha3 chimera]]
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__TOC__
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[[Category: bacteriophage phix174]]
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</StructureSection>
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[[Category: icosahedral virus]]
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[[Category: Escherichia phage alpha3]]
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[[Category: microviridae]]
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[[Category: Escherichia virus phiX174]]
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[[Category: phix174]]
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[[Category: Large Structures]]
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[[Category: three-dimentional structure]]
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[[Category: Bernal RA]]
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[[Category: virion]]
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[[Category: Esmeralda R]]
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[[Category: Fane BA]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:49:04 2008''
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[[Category: Hafenstein S]]
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[[Category: Rossmann MG]]

Current revision

The phiX174 DNA binding protein J in two different capsid environments.

PDB ID 1rb8

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