6qyj

From Proteopedia

(Difference between revisions)

Current revision

The cryo-EM structure of the connector of the mature bacteriophage phi29

6qyj, resolution 3.40Å

Structural highlights

6qyj 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:	Electron Microscopy, Resolution 3.4Å
Experimental data:	Check to display Experimental Data
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 mature virion of the tailed bacteriophage varphi29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile tail. Here, we report the near-atomic structures of the varphi29 pre-genome packaging head (prohead), the mature virion and the genome-emptied virion. Structural comparisons suggest local rotation or oscillation of the head-tail connector upon DNA packaging and release. Termination of the DNA packaging occurs through pressure-dependent correlative positional and conformational changes in the connector. The funnel-shaped tail lower collar attaches the expanded narrow end of the connector and has a 180-A long, 24-strand beta barrel narrow stem tube that undergoes conformational changes upon genome release. The appendages form an interlocked assembly attaching the tail around the collar. The membrane active long loops at the distal end of the tail knob exit during the late stage of infection and form the cone-shaped tip of a largely hydrophobic helix barrel, prepared for membrane penetration.

Structural assembly of the tailed bacteriophage varphi29.,Xu J, Wang D, Gui M, Xiang Y Nat Commun. 2019 May 30;10(1):2366. doi: 10.1038/s41467-019-10272-3. PMID:31147544^[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
↑ Xu J, Wang D, Gui M, Xiang Y. Structural assembly of the tailed bacteriophage varphi29. Nat Commun. 2019 May 30;10(1):2366. doi: 10.1038/s41467-019-10272-3. PMID:31147544 doi:http://dx.doi.org/10.1038/s41467-019-10272-3

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6qyj"

@@ Line 3: / Line 3: @@
 <SX load='6qyj' size='340' side='right' viewer='molstar' caption='[[6qyj]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6qyj]] is a 12 chain structure with 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=6QYJ OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6QYJ FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6qyj]] 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=6QYJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QYJ FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6qyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qyj OCA], [http://pdbe.org/6qyj PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qyj RCSB], [http://www.ebi.ac.uk/pdbsum/6qyj PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qyj ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.4&#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=6qyj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qyj OCA], [https://pdbe.org/6qyj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qyj RCSB], [https://www.ebi.ac.uk/pdbsum/6qyj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qyj ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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>
+[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 19: / Line 20: @@
 ==See Also==
-*[[Thymidylate synthase 3D structures|Thymidylate synthase 3D structures]]
+*[[Portal protein 3D structures|Portal protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </SX>
-[[Category: Bacillus phage phi29]]
+[[Category: Bacillus virus phi29]]
 [[Category: Large Structures]]
-[[Category: Gui, M]]
+[[Category: Gui M]]
-[[Category: Wang, D]]
+[[Category: Wang D]]
-[[Category: Xiang, Y]]
+[[Category: Xiang Y]]
-[[Category: Xu, J]]
+[[Category: Xu J]]
-[[Category: Bacteriophage]]
-[[Category: Phi29]]
-[[Category: Prohead]]
-[[Category: Virus]]

6qyj

From Proteopedia

Current revision

The cryo-EM structure of the connector of the mature bacteriophage phi29

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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