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1ijg

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Structure of the Bacteriophage phi29 Head-Tail Connector Protein

Structural highlights

1ijg is a 12 chain structure with sequence from Bacillus virus phi29. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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]^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

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 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^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Simpson AA, Tao Y, Leiman PG, Badasso MO, He Y, Jardine PJ, Olson NH, Morais MC, Grimes S, Anderson DL, Baker TS, Rossmann MG. Structure of the bacteriophage phi29 DNA packaging motor. Nature. 2000 Dec 7;408(6813):745-50. PMID:11130079 doi:10.1038/35047129
↑ Guasch A, Pous J, Ibarra B, Gomis-Ruth FX, Valpuesta JM, Sousa N, Carrascosa JL, Coll M. Detailed architecture of a DNA translocating machine: the high-resolution structure of the bacteriophage phi29 connector particle. J Mol Biol. 2002 Jan 25;315(4):663-76. PMID:11812138 doi:http://dx.doi.org/10.1006/jmbi.2001.5278
↑ Xiao F, Moll WD, Guo S, Guo P. Binding of pRNA to the N-terminal 14 amino acids of connector protein of bacteriophage phi29. Nucleic Acids Res. 2005 May 10;33(8):2640-9. doi: 10.1093/nar/gki554. Print 2005. PMID:15886394 doi:http://dx.doi.org/10.1093/nar/gki554
↑ Fu CY, Prevelige PE Jr. In vitro incorporation of the phage Phi29 connector complex. Virology. 2009 Nov 10;394(1):149-53. doi: 10.1016/j.virol.2009.08.016. Epub 2009 , Sep 9. PMID:19744688 doi:http://dx.doi.org/10.1016/j.virol.2009.08.016
↑ Grimes S, Ma S, Gao J, Atz R, Jardine PJ. Role of phi29 connector channel loops in late-stage DNA packaging. J Mol Biol. 2011 Jul 1;410(1):50-9. doi: 10.1016/j.jmb.2011.04.070. Epub 2011 May, 5. PMID:21570409 doi:http://dx.doi.org/10.1016/j.jmb.2011.04.070
↑ Ibarra B, Caston JR, Llorca O, Valle M, Valpuesta JM, Carrascosa JL. Topology of the components of the DNA packaging machinery in the phage phi29 prohead. J Mol Biol. 2000 May 19;298(5):807-15. doi: 10.1006/jmbi.2000.3712. PMID:10801350 doi:http://dx.doi.org/10.1006/jmbi.2000.3712
↑ Simpson AA, Leiman PG, Tao Y, He Y, Badasso MO, Jardine PJ, Anderson DL, Rossmann MG. Structure determination of the head-tail connector of bacteriophage phi29. Acta Crystallogr D Biol Crystallogr. 2001 Sep;57(Pt 9):1260-9. Epub 2001, Aug 23. PMID:11526317

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1ijg"

@@ Line 3: / Line 3: @@
 <StructureSection load='1ijg' size='340' side='right'caption='[[1ijg]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ijg]] is a 12 chain structure. 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>
+<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>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1fou|1fou]], [[1foq|1foq]]</div></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]] 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>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/VG10_BPPH2 VG10_BPPH2]] This protein is located between the head and the tail of this bacteriophage.
+[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 ==
@@ Line 22: / Line 22: @@
 __TOC__
 </StructureSection>
+[[Category: Bacillus virus phi29]]
 [[Category: Large Structures]]
-[[Category: Anderson, D L]]
+[[Category: Anderson DL]]
-[[Category: Badasso, M]]
+[[Category: Badasso M]]
-[[Category: He, Y]]
+[[Category: He Y]]
-[[Category: Jardine, P J]]
+[[Category: Jardine PJ]]
-[[Category: Leiman, P G]]
+[[Category: Leiman PG]]
-[[Category: Rossmann, M G]]
+[[Category: Rossmann MG]]
-[[Category: Simpson, A A]]
+[[Category: Simpson AA]]
-[[Category: Tao, Y]]
+[[Category: Tao Y]]
-[[Category: Alpha-helical bundle]]
-[[Category: Rna binding motif]]
-[[Category: Viral protein]]

1ijg

From Proteopedia

Current revision

Structure of the Bacteriophage phi29 Head-Tail Connector Protein

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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