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<StructureSection load='7ook' size='340' side='right'caption='[[7ook]], [[Resolution|resolution]] 2.23&Aring;' scene=''>
<StructureSection load='7ook' size='340' side='right'caption='[[7ook]], [[Resolution|resolution]] 2.23&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[7ook]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_prd1 Enterobacteria phage prd1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OOK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OOK FirstGlance]. <br>
<table><tr><td colspan='2'>[[7ook]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Enterobacteria_phage_PRD1 Enterobacteria phage PRD1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7OOK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7OOK FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=Z80:3-(2-CHLORO-10H-PHENOTHIAZIN-10-YL)-N,N-DIMETHYLPROPAN-1-AMINE'>Z80</scene></td></tr>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=Z80:3-(2-CHLORO-10H-PHENOTHIAZIN-10-YL)-N,N-DIMETHYLPROPAN-1-AMINE'>Z80</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=7ook FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ook OCA], [https://pdbe.org/7ook PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ook RCSB], [https://www.ebi.ac.uk/pdbsum/7ook PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ook 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=7ook FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7ook OCA], [https://pdbe.org/7ook PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7ook RCSB], [https://www.ebi.ac.uk/pdbsum/7ook PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7ook ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/CAPSD_BPPRD CAPSD_BPPRD]] Major capsid protein self-assembles to form an icosahedral capsid with a pseudo T=25 symmetry, about 66 nm in diameter, and consisting of 240 capsid proteins trimers. The capsid encapsulates an inner membrane and the genomic dsDNA genome. The major coat protein P3 and two assembly factors (P10 and P17) are needed during the assembly of the virus particle inside the host cell, when the capsid protein multimers are capable of enclosing the host-derived membrane, containing the virus-encoded membrane-associated proteins.  
[[https://www.uniprot.org/uniprot/CAPSD_BPPRD CAPSD_BPPRD]] Major capsid protein self-assembles to form an icosahedral capsid with a pseudo T=25 symmetry, about 66 nm in diameter, and consisting of 240 capsid proteins trimers. The capsid encapsulates an inner membrane and the genomic dsDNA genome. The major coat protein P3 and two assembly factors (P10 and P17) are needed during the assembly of the virus particle inside the host cell, when the capsid protein multimers are capable of enclosing the host-derived membrane, containing the virus-encoded membrane-associated proteins.
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
P3 has been imaged with X-ray crystallography to reveal a trimeric molecule with strikingly similar characteristics to hexon, the major coat protein of adenovirus. The structure of native P3 has now been extended to 1.65 A resolution (R(work) = 19.0% and R(free) = 20.8%). The new high-resolution model shows that P3 forms crystals through hydrophobic patches solvated by 2-methyl-2,4-pentanediol molecules. It reveals details of how the molecule's high stability may be achieved through ordered solvent in addition to intra- and intersubunit interactions. Of particular importance is a 'puddle' at the top of the molecule containing a four-layer deep hydration shell that cross-links a complex structural feature formed by 'trimerization loops'. These loops also link subunits by extending over a neighbor to reach the third subunit in the trimer. As each subunit has two eight-stranded viral jelly rolls, the trimer has a pseudo-hexagonal shape to allow close packing in its 240 hexavalent capsid positions. Flexible regions in P3 facilitate these interactions within the capsid and with the underlying membrane. A selenometh-ionine P3 derivative, with which the structure was solved, has been refined to 2.2 A resolution (R(work) = 20.1% and R(free) = 22.8%). The derivatized molecule is essentially unchanged, although synchrotron radiation has the curious effect of causing it to rotate about its threefold axis. P3 is a second example of a trimeric 'double-barrel' protein that forms a stable building block with optimal shape for constructing a large icosahedral viral capsid. A major difference is that hexon has long variable loops that distinguish different adenovirus species. The short loops in P3 and the severe constraints of its various interactions explain why the PRD1 family has highly conserved coat proteins.
 
The X-ray crystal structure of P3, the major coat protein of the lipid-containing bacteriophage PRD1, at 1.65 A resolution.,Benson SD, Bamford JK, Bamford DH, Burnett RM Acta Crystallogr D Biol Crystallogr. 2002 Jan;58(Pt 1):39-59. Epub 2001, Dec 21. PMID:11752778<ref>PMID:11752778</ref>
 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 7ook" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Enterobacteria phage prd1]]
[[Category: Enterobacteria phage PRD1]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Abrescia, N G.A]]
[[Category: Abrescia NGA]]
[[Category: Duyvesteyn, H M.E]]
[[Category: Duyvesteyn HME]]
[[Category: Jimenez-Oses, G]]
[[Category: Jimenez-Oses G]]
[[Category: Martinez-Castillo, A]]
[[Category: Martinez-Castillo A]]
[[Category: Oksanen, H M]]
[[Category: Oksanen HM]]
[[Category: Peccati, F]]
[[Category: Peccati F]]
[[Category: Stuart, D I]]
[[Category: Stuart DI]]
[[Category: Protein complex]]
[[Category: Viral protein]]

Revision as of 09:23, 8 September 2022

Bacteriophage PRD1 Major Capsid Protein P3 in complex with CPZBacteriophage PRD1 Major Capsid Protein P3 in complex with CPZ

Structural highlights

7ook is a 3 chain structure with sequence from Enterobacteria phage PRD1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:, , ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[CAPSD_BPPRD] Major capsid protein self-assembles to form an icosahedral capsid with a pseudo T=25 symmetry, about 66 nm in diameter, and consisting of 240 capsid proteins trimers. The capsid encapsulates an inner membrane and the genomic dsDNA genome. The major coat protein P3 and two assembly factors (P10 and P17) are needed during the assembly of the virus particle inside the host cell, when the capsid protein multimers are capable of enclosing the host-derived membrane, containing the virus-encoded membrane-associated proteins.

7ook, resolution 2.23Å

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OCA
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