4kz2: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[4kz2]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KZ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KZ2 FirstGlance]. <br>
<table><tr><td colspan='2'>[[4kz2]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4KZ2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4KZ2 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></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]] 3.05&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=4kz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kz2 OCA], [https://pdbe.org/4kz2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kz2 RCSB], [https://www.ebi.ac.uk/pdbsum/4kz2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kz2 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=4kz2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4kz2 OCA], [https://pdbe.org/4kz2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4kz2 RCSB], [https://www.ebi.ac.uk/pdbsum/4kz2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4kz2 ProSAT]</span></td></tr>
</table>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The bacteriophage phi29 DNA packaging motor, one of the strongest biological motors characterized to date, is geared by a packaging RNA (pRNA) ring. When assembled from three RNA fragments, its three-way junction (3WJ) motif is highly thermostable, is resistant to 8 M urea, and remains associated at extremely low concentrations in vitro and in vivo. To elucidate the structural basis for its unusual stability, we solved the crystal structure of this pRNA 3WJ motif at 3.05 A. The structure revealed two divalent metal ions that coordinate 4 nt of the RNA fragments. Single-molecule fluorescence resonance energy transfer (smFRET) analysis confirmed a structural change of 3WJ upon addition of Mg(2+). The reported pRNA 3WJ conformation is different from a previously published construct that lacks the metal coordination sites. The phi29 DNA packaging motor contains a dodecameric connector at the vertex of the procapsid, with a central pore for DNA translocation. This portal connector serves as the foothold for pRNA binding to procapsid. Subsequent modeling of a connector/pRNA complex suggests that the pRNA of the phi29 DNA packaging motor exists as a hexameric complex serving as a sheath over the connector. The model of hexameric pRNA on the connector agrees with AFM images of the phi29 pRNA hexamer acquired in air and matches all distance parameters obtained from cross-linking, complementary modification, and chemical modification interference.
Crystal structure of 3WJ core revealing divalent ion-promoted thermostability and assembly of the Phi29 hexameric motor pRNA.,Zhang H, Endrizzi JA, Shu Y, Haque F, Sauter C, Shlyakhtenko LS, Lyubchenko Y, Guo P, Chi YI RNA. 2013 Sep;19(9):1226-37. doi: 10.1261/rna.037077.112. Epub 2013 Jul 24. PMID:23884902<ref>PMID:23884902</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 4kz2" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Chi, Y I]]
[[Category: Chi Y-I]]
[[Category: Endrizzi, J A]]
[[Category: Endrizzi JA]]
[[Category: Guo, P]]
[[Category: Guo P]]
[[Category: Haque, F]]
[[Category: Haque F]]
[[Category: Sauter, C]]
[[Category: Sauter C]]
[[Category: Shu, Y]]
[[Category: Shu Y]]
[[Category: Zhang, H]]
[[Category: Zhang H]]
[[Category: Phi29 dna packaging motor prna core element]]
[[Category: Rna]]

Latest revision as of 12:16, 1 March 2024

Crystal Structure of phi29 pRNA 3WJ Core

4kz2, resolution 3.05Å

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