1cd3: Difference between revisions

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:1cd3.gif|left|200px]]<br />
-<applet load="1cd3" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1cd3, resolution 3.5&Aring;" />
-'''PROCAPSID OF BACTERIOPHAGE PHIX174'''<br />
-==Overview==
+==PROCAPSID OF BACTERIOPHAGE PHIX174==
-An empty precursor particle called the procapsid is formed during assembly, of the single-stranded DNA bacteriophage phiX174. Assembly of the phiX174, procapsid requires the presence of the two scaffolding proteins, D and B, which are structural components of the procapsid, but are not found in the, mature virion. The X-ray crystallographic structure of a "closed", procapsid particle has been determined to 3.5 A resolution. This structure, has an external scaffold made from 240 copies of protein D, 60 copies of, the internally located B protein, and contains 60 copies of each of the, viral structural proteins F and G, which comprise the shell and the 5-fold, spikes, respectively. The F capsid protein has a similar conformation to, that seen in the mature virion, and differs from the previously determined, 25 A resolution electron microscopic reconstruction of the "open", procapsid, in which the F protein has a different conformation. The D, scaffolding protein has a predominantly alpha-helical fold and displays, remarkable conformational variability. We report here an improved and, refined structure of the closed procapsid and describe in some detail the, differences between the four independent D scaffolding proteins per, icosahedral asymmetric unit, as well as their interaction with the F, capsid protein. We re-analyze and correct the comparison of the closed, procapsid with the previously determined cryo-electron microscopic image, reconstruction of the open procapsid and discuss the major structural, rearrangements that must occur during assembly. A model is proposed in, which the D proteins direct the assembly process by sequential binding and, conformational switching.
+<StructureSection load='1cd3' size='340' side='right'caption='[[1cd3]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
+== Structural highlights ==
-==About this Structure==
+<table><tr><td colspan='2'>[[1cd3]] is a 7 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_phiX174 Escherichia virus phiX174]. The February 2000 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Bacteriophage phiX174''  by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2000_2 10.2210/rcsb_pdb/mom_2000_2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CD3 FirstGlance]. <br>
-CD3 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_phix174 Enterobacteria phage phix174]. The following page contains interesting information on the relation of 1CD3 with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb2_1.html Bacteriophage phiX174]]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1CD3 OCA].
+</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>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1cd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cd3 OCA], [https://pdbe.org/1cd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cd3 RCSB], [https://www.ebi.ac.uk/pdbsum/1cd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cd3 ProSAT]</span></td></tr>
-==Reference==
+</table>
-The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus phiX174., Dokland T, Bernal RA, Burch A, Pletnev S, Fane BA, Rossmann MG, J Mol Biol. 1999 May 14;288(4):595-608. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10329166 10329166]
+== Function ==
+[https://www.uniprot.org/uniprot/CAPSD_BPPHS CAPSD_BPPHS] Assembles to form an icosahedral capsid with a T=1 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins F (PubMed:11991963, PubMed:1370343, PubMed:8158636). 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 (PubMed:29229840). After the genome had been ejected, the channel formed by the F proteins at the unique fivefold axis remains open (PubMed:29229840).<ref>PMID:11991963</ref> <ref>PMID:1370343</ref> <ref>PMID:29229840</ref> <ref>PMID:8158636</ref>
+== 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/cd/1cd3_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=1cd3 ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Bacteriophage phiX174]]
-[[Category: Enterobacteria phage phix174]]
+[[Category: Escherichia virus phiX174]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Dokland, T.]]
+[[Category: RCSB PDB Molecule of the Month]]
-[[Category: Rossmann, M.G.]]
+[[Category: Dokland T]]
-[[Category: bacteriophage]]
+[[Category: Rossmann MG]]
-[[Category: chaperone]]
-[[Category: complex (virus capsid proteins)]]
-[[Category: icosahedral virus]]
-[[Category: procapsid]]
-[[Category: scaffolding protein]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 08:58:14 2007''