1cd3: Difference between revisions

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 ==PROCAPSID OF BACTERIOPHAGE PHIX174==
-<StructureSection load='1cd3' size='340' side='right' caption='[[1cd3]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
+<StructureSection load='1cd3' size='340' side='right'caption='[[1cd3]], [[Resolution|resolution]] 3.50&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1cd3]] is a 7 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpphx Bpphx]. The February 2000 RCSB PDB [http://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 [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CD3 FirstGlance]. <br>
+<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>
-</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=1cd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cd3 OCA], [http://pdbe.org/1cd3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1cd3 RCSB], [http://www.ebi.ac.uk/pdbsum/1cd3 PDBsum]</span></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]] 3.5&#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>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/B_BPPHX B_BPPHX]] Participates in the assembly of the viral procapsid in the cytoplasm. Forms first a 12S pre-assembly complex with protein H, and F and G pentamers, then twelve 12S complexes are joined by the D protein to form the procapsid. Internal scaffold protein B is released from the procapsid upon genome packaging, possibly through affinity displacement by the protein J, or by proteolysis. [[http://www.uniprot.org/uniprot/D_BPPHX D_BPPHX]] Assembles the procapsid by joining twelve 12S pre-assembly complex into a T=1 icosahedral particle, called 108S procapsid. Ten proteins D bind each 12S complex, which are formed by three pentamers of F, G, B protein and a H protein. The scaffolding protein is released from the provirion after genome packaging to form the mature virion.<ref>PMID:159449</ref> <ref>PMID:15890913</ref>  [[http://www.uniprot.org/uniprot/G_BPPHX G_BPPHX]] Attaches the circulating virion to the bacterial lipopolysaccharides which serve as receptor for the virus. Determines the phage host-range. Probably triggers with protein H the injection of the phage DNA into the host cytoplasm upon conformational changes induced by the interaction with host lipopolysaccharides.<ref>PMID:10739948</ref> <ref>PMID:14553915</ref>  [[http://www.uniprot.org/uniprot/F_BPPHX F_BPPHX]] Assembles to form an icosahedral capsid with a T=1 symmetry, about 30 nm in diameter, and consisting of 60 capsid proteins F.<ref>PMID:11991963</ref>
+[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>
+     <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>
@@ Line 17: / Line 19: @@
 </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>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-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.
-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:10329166<ref>PMID:10329166</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1cd3" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 31: / Line 24: @@
 </StructureSection>
 [[Category: Bacteriophage phiX174]]
-[[Category: Bpphx]]
+[[Category: Escherichia virus phiX174]]
+[[Category: Large Structures]]
 [[Category: RCSB PDB Molecule of the Month]]
-[[Category: Dokland, T]]
+[[Category: Dokland T]]
-[[Category: Rossmann, M G]]
+[[Category: Rossmann MG]]
-[[Category: Bacteriophage]]
-[[Category: Chaperone]]
-[[Category: Icosahedral virus]]
-[[Category: Procapsid]]
-[[Category: Scaffolding protein]]
-[[Category: Virus]]