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| - | [[Image:1h5w.jpg|left|200px]]<br /><applet load="1h5w" size="450" color="white" frame="true" align="right" spinBox="true" | |
| - | caption="1h5w, resolution 2.1Å" /> | |
| - | '''2.1A BACTERIOPHAGE PHI-29 CONNECTOR'''<br /> | |
| | | | |
| - | ==Overview== | + | ==2.1A Bacteriophage Phi-29 Connector== |
| - | The three-dimensional crystal structure of the bacteriophage phi29, connector has been solved and refined to 2.1A resolution. This 422 kDa, oligomeric protein connects the head of the phage to its tail and, translocates the DNA into the prohead during packaging. Each monomer has, an elongated shape and is composed of a central, mainly alpha-helical, domain that includes a three-helix bundle, a distal alpha/beta domain and, a proximal six-stranded SH3-like domain. The protomers assemble into a, 12-mer, propeller-like, super-structure with a 35 A wide central channel., The surface of the channel is mainly electronegative, but it includes two, lysine rings 20 A apart. On the external surface of the particle a, hydrophobic belt extends to the concave area below the SH3-like domain, which forms a crown that retains the particle in the head. The lipophilic, belt contacts the non-matching symmetry vertex of the capsid and forms a, bearing for the connector rotation. The structure suggests a translocation, mechanism in which the longitudinal displacement of the DNA along its axis, is coupled to connector spinning. | + | <StructureSection load='1h5w' size='340' side='right'caption='[[1h5w]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | + | == Structural highlights == |
| | + | <table><tr><td colspan='2'>[[1h5w]] is a 3 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=1H5W OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H5W FirstGlance]. <br> |
| | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> |
| | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=1h5w FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h5w OCA], [https://pdbe.org/1h5w PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h5w RCSB], [https://www.ebi.ac.uk/pdbsum/1h5w PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h5w ProSAT]</span></td></tr> |
| | + | </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 three-dimensional crystal structure of the bacteriophage phi29 connector has been solved and refined to 2.1A resolution. This 422 kDa oligomeric protein connects the head of the phage to its tail and translocates the DNA into the prohead during packaging. Each monomer has an elongated shape and is composed of a central, mainly alpha-helical domain that includes a three-helix bundle, a distal alpha/beta domain and a proximal six-stranded SH3-like domain. The protomers assemble into a 12-mer, propeller-like, super-structure with a 35 A wide central channel. The surface of the channel is mainly electronegative, but it includes two lysine rings 20 A apart. On the external surface of the particle a hydrophobic belt extends to the concave area below the SH3-like domain, which forms a crown that retains the particle in the head. The lipophilic belt contacts the non-matching symmetry vertex of the capsid and forms a bearing for the connector rotation. The structure suggests a translocation mechanism in which the longitudinal displacement of the DNA along its axis is coupled to connector spinning. |
| | | | |
| - | ==About this Structure==
| + | Detailed architecture of a DNA translocating machine: the high-resolution structure of the bacteriophage phi29 connector particle.,Guasch A, Pous J, Ibarra B, Gomis-Ruth FX, Valpuesta JM, Sousa N, Carrascosa JL, Coll M J Mol Biol. 2002 Jan 25;315(4):663-76. PMID:11812138<ref>PMID:11812138</ref> |
| - | 1H5W is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Vibrio_phage_f237 Vibrio phage f237] with MPD as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1H5W OCA].
| + | |
| | | | |
| - | ==Reference==
| + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| - | Detailed architecture of a DNA translocating machine: the high-resolution structure of the bacteriophage phi29 connector particle., Guasch A, Pous J, Ibarra B, Gomis-Ruth FX, Valpuesta JM, Sousa N, Carrascosa JL, Coll M, J Mol Biol. 2002 Jan 25;315(4):663-76. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11812138 11812138]
| + | </div> |
| - | [[Category: Single protein]] | + | <div class="pdbe-citations 1h5w" style="background-color:#fffaf0;"></div> |
| - | [[Category: Vibrio phage f237]] | + | == References == |
| - | [[Category: Carrascosa, J.L.]] | + | <references/> |
| - | [[Category: Coll, M.]] | + | __TOC__ |
| - | [[Category: Gomis-Ruth, F.X.]] | + | </StructureSection> |
| - | [[Category: Guasch, A.]] | + | [[Category: Bacillus virus phi29]] |
| - | [[Category: Ibarra, B.]] | + | [[Category: Large Structures]] |
| - | [[Category: Pous, J.]] | + | [[Category: Carrascosa JL]] |
| - | [[Category: Sousa, N.]] | + | [[Category: Coll M]] |
| - | [[Category: Valpuesta, J.M.]] | + | [[Category: Gomis-Ruth FX]] |
| - | [[Category: MPD]]
| + | [[Category: Guasch A]] |
| - | [[Category: connector]]
| + | [[Category: Ibarra B]] |
| - | [[Category: helix bundle]]
| + | [[Category: Pous J]] |
| - | [[Category: portal]]
| + | [[Category: Sousa N]] |
| - | [[Category: sh3-like]]
| + | [[Category: Valpuesta JM]] |
| - | [[Category: virus]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 16:25:49 2007''
| + | |
| Structural highlights
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 three-dimensional crystal structure of the bacteriophage phi29 connector has been solved and refined to 2.1A resolution. This 422 kDa oligomeric protein connects the head of the phage to its tail and translocates the DNA into the prohead during packaging. Each monomer has an elongated shape and is composed of a central, mainly alpha-helical domain that includes a three-helix bundle, a distal alpha/beta domain and a proximal six-stranded SH3-like domain. The protomers assemble into a 12-mer, propeller-like, super-structure with a 35 A wide central channel. The surface of the channel is mainly electronegative, but it includes two lysine rings 20 A apart. On the external surface of the particle a hydrophobic belt extends to the concave area below the SH3-like domain, which forms a crown that retains the particle in the head. The lipophilic belt contacts the non-matching symmetry vertex of the capsid and forms a bearing for the connector rotation. The structure suggests a translocation mechanism in which the longitudinal displacement of the DNA along its axis is coupled to connector spinning.
Detailed architecture of a DNA translocating machine: the high-resolution structure of the bacteriophage phi29 connector particle.,Guasch A, Pous J, Ibarra B, Gomis-Ruth FX, Valpuesta JM, Sousa N, Carrascosa JL, Coll M J Mol Biol. 2002 Jan 25;315(4):663-76. PMID:11812138[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
- ↑ 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
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