1hqn
From Proteopedia
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| - | [[Image:1hqn.jpg|left|200px]]<br /><applet load="1hqn" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="1hqn, resolution 2.20Å" /> | ||
| - | '''THE SELENOMETHIONINE DERIVATIVE OF P3, THE MAJOR COAT PROTEIN OF THE LIPID-CONTAINING BACTERIOPHAGE PRD1.'''<br /> | ||
| - | == | + | ==THE SELENOMETHIONINE DERIVATIVE OF P3, THE MAJOR COAT PROTEIN OF THE LIPID-CONTAINING BACTERIOPHAGE PRD1.== |
| + | <StructureSection load='1hqn' size='340' side='right'caption='[[1hqn]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[1hqn]] 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=1HQN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HQN FirstGlance]. <br> | ||
| + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=1hqn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hqn OCA], [https://pdbe.org/1hqn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hqn RCSB], [https://www.ebi.ac.uk/pdbsum/1hqn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hqn ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == 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. | ||
| + | <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. | 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | [[Category: Enterobacteria phage | + | <div class="pdbe-citations 1hqn" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | == References == |
| - | [[Category: Bamford | + | <references/> |
| - | [[Category: Bamford | + | __TOC__ |
| - | [[Category: Benson | + | </StructureSection> |
| - | [[Category: Burnett | + | [[Category: Enterobacteria phage PRD1]] |
| - | + | [[Category: Large Structures]] | |
| - | + | [[Category: Bamford DH]] | |
| - | + | [[Category: Bamford JKH]] | |
| - | + | [[Category: Benson SD]] | |
| - | + | [[Category: Burnett RM]] | |
| - | + | ||
Current revision
THE SELENOMETHIONINE DERIVATIVE OF P3, THE MAJOR COAT PROTEIN OF THE LIPID-CONTAINING BACTERIOPHAGE PRD1.
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