View source for 1gff


==THE ATOMIC STRUCTURE OF THE DEGRADED PROCAPSID PARTICLE OF THE BACTERIOPHAGE G4: INDUCED STRUCTURAL CHANGES IN THE PRESENCE OF CALCIUM IONS AND FUNCTIONAL IMPLICATIONS==
<StructureSection load='1gff' size='340' side='right'caption='[[1gff]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1gff]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_phage_G4 Escherichia phage G4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1GFF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1GFF FirstGlance]. <br>
</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&#8491;</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=1gff FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1gff OCA], [https://pdbe.org/1gff PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1gff RCSB], [https://www.ebi.ac.uk/pdbsum/1gff PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1gff ProSAT]</span></td></tr>
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== Function ==
[https://www.uniprot.org/uniprot/CAPSD_BPG4 CAPSD_BPG4] 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]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gf/1gff_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1gff ConSurf].
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== Publication Abstract from PubMed ==
Bacteriophage G4 and phiX174 are members of the Microviridae family. The degree of similarity of the structural proteins ranges from 66% identity of the F protein to 40% identity of the G protein. The atomic structure of the phiX174 virion had previously been determined by X-ray crystallography. Bacteriophage G4 procapsids, consisting of the structural proteins F, G, D, B, H, and small traces of J but no DNA, were set up for crystallization. However, the resultant crystals were of degraded procapsid particles, which had lost the assembly scaffolding proteins D and B, resulting in particles that resembled empty virions. The structure of the degraded G4 procapsid has been determined to 3.0 angstrom resolution. The particles crystallized in the hexagonal space group P6(3)22 with unit cell dimensions a=b=414.2(5) angstrom and c=263.0(3) angstrom. The diffraction data were collected at the Cornell High Energy Synchrotron Source (CHESS) on film and image plates using oscillation photography. Packing considerations indicated there were two particles per unit cell. A self-rotation function confirmed that the particles were positioned on 32 point group special positions in the unit cell. Initial phases were calculated to 6 angstrom resolution, based on the known phiX174 virion model. Phase information was then extended in steps to 3.0 angstrom resolution by molecular replacement electron density modification and particle envelope generation. The resulting electron density map was readily interpretable in terms of the F and G polypeptides, as occur in the mature capsid of phiX174. In a few regions of the electron density map there were inconsistencies between the density and the published amino acid sequence. Redetermining the amino acid sequence confirmed that the density was correct. The r.m.s. deviation between the Calpha backbone of the mature capsid of phiX174 and the degraded G4 procapsid was 0.36 angstrom for the F protein and 1.38 angstrom for the G protein. This is consistent with the greater conservation of the F protein compared to the G protein sequences among members of the Microviridae family. Functionally important features between phiX174 and G4 had greater conservation. Calcium ions (Ca2+) were shown to bind to G4 at a general site located near the icosahedral 3-fold axis on the F protein capsid, equivalent to sites found previously in phiX174. Binding of Ca2+ also caused the ordering of the conserved region of the DNA binding protein J, which was present in the degraded procapsid particle in the absence of DNA.

Atomic structure of the degraded procapsid particle of the bacteriophage G4: induced structural changes in the presence of calcium ions and functional implications.,McKenna R, Bowman BR, Ilag LL, Rossmann MG, Fane BA J Mol Biol. 1996 Mar 8;256(4):736-50. PMID:8642594<ref>PMID:8642594</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia phage G4]]
[[Category: Large Structures]]
[[Category: Rossmann MG]]