1ijg: Difference between revisions

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-{{Seed}}
-[[Image:1ijg.png|left|200px]]
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+==Structure of the Bacteriophage phi29 Head-Tail Connector Protein==
-The line below this paragraph, containing "STRUCTURE_1ijg", creates the "Structure Box" on the page.
+<StructureSection load='1ijg' size='340' side='right'caption='[[1ijg]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[1ijg]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_virus_phi29 Bacillus virus phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IJG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IJG FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.9&#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=1ijg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ijg OCA], [https://pdbe.org/1ijg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ijg RCSB], [https://www.ebi.ac.uk/pdbsum/1ijg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ijg ProSAT]</span></td></tr>
-{{STRUCTURE_1ijg|  PDB=1ijg  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PORTL_BPPH2 PORTL_BPPH2] Forms the portal vertex of the capsid (PubMed:10801350) (PubMed:19744688, PubMed:21570409). This portal plays critical roles in head assembly, genome packaging, neck/tail attachment, and genome ejection (By similarity). The portal protein multimerizes as a single ring-shaped homododecamer arranged around a central channel (PubMed:11812138, PubMed:21570409). Binds to the 6 packaging RNA molecules (pRNA) forming a double-ring structure which in turn binds to the ATPase gp16 hexamer, forming the active DNA-translocating motor (PubMed:15886394, PubMed:11130079). This complex is essential for the specificity of packaging from the left DNA end.[UniProtKB:P13334]<ref>PMID:11130079</ref> <ref>PMID:11812138</ref> <ref>PMID:15886394</ref> <ref>PMID:19744688</ref> <ref>PMID:21570409</ref> <ref>PMID:10801350</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The head-tail connector of bacteriophage phi29 is composed of 12 36 kDa subunits with 12-fold symmetry. It is the central component of a rotary motor that packages the genomic dsDNA into preformed proheads. This motor consists of the head-tail connector, surrounded by a phi29-encoded, 174-base, RNA and a viral ATPase protein, both of which have fivefold symmetry in three-dimensional cryo-electron microscopy reconstructions. DNA is translocated into the prohead through a 36 A diameter pore in the center of the connector, where the DNA takes the role of a motor spindle. The helical nature of the DNA allows the rotational action of the connector to be transformed into a linear translation of the DNA. The crystal structure determination of connector crystals in space group C2 was initiated by molecular replacement, using an approximately 20 A resolution model derived from cryo-electron microscopy. The model phases were extended to 3.5 A resolution using 12-fold non-crystallographic symmetry averaging and solvent flattening. Although this electron density was not interpretable, the phases were adequate to locate the position of 24 mercury sites of a thimerosal heavy-atom derivative. The resultant 3.2 A single isomorphous replacement phases were improved using density modification, producing an interpretable electron-density map. The crystallographically refined structure was used as a molecular-replacement model to solve the structures of two other crystal forms of the connector molecule. One of these was in the same space group and almost isomorphous, whereas the other was in space group P2(1)2(1)2. The structural differences between the oligomeric connector molecules in the three crystal forms and between different monomers within each crystal show that the structure is relatively flexible, particularly in the protruding domain at the wide end of the connector. This domain probably acts as a bearing, allowing the connector to rotate within the pentagonal portal of the prohead during DNA packaging.
-===Structure of the Bacteriophage phi29 Head-Tail Connector Protein===
+Structure determination of the head-tail connector of bacteriophage phi29.,Simpson AA, Leiman PG, Tao Y, He Y, Badasso MO, Jardine PJ, Anderson DL, Rossmann MG Acta Crystallogr D Biol Crystallogr. 2001 Sep;57(Pt 9):1260-9. Epub 2001, Aug 23. PMID:11526317<ref>PMID:11526317</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_11526317}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 1ijg" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 11526317 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_11526317}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Bacillus virus phi29]]
-IJG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_phage_phi29 Bacillus phage phi29]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IJG OCA].
+[[Category: Large Structures]]
+[[Category: Anderson DL]]
-==Reference==
+[[Category: Badasso M]]
-Structure determination of the head-tail connector of bacteriophage phi29., Simpson AA, Leiman PG, Tao Y, He Y, Badasso MO, Jardine PJ, Anderson DL, Rossmann MG, Acta Crystallogr D Biol Crystallogr. 2001 Sep;57(Pt 9):1260-9. Epub 2001, Aug 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11526317 11526317]
+[[Category: He Y]]
-[[Category: Bacillus phage phi29]]
+[[Category: Jardine PJ]]
-[[Category: Single protein]]
+[[Category: Leiman PG]]
-[[Category: Anderson, D L.]]
+[[Category: Rossmann MG]]
-[[Category: Badasso, M.]]
+[[Category: Simpson AA]]
-[[Category: He, Y.]]
+[[Category: Tao Y]]
-[[Category: Jardine, P J.]]
-[[Category: Leiman, P G.]]
-[[Category: Rossmann, M G.]]
-[[Category: Simpson, A A.]]
-[[Category: Tao, Y.]]
-[[Category: Alpha-helical bundle]]
-[[Category: Rna binding motif]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul  1 12:20:20 2008''