6i9e

From Proteopedia

(Difference between revisions)

Current revision

Thermophage P23-45 empty expanded capsid

6i9e, resolution 3.74Å

Structural highlights

6i9e is a 14 chain structure with sequence from Thermus virus P23-45. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 3.74Å
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CAPSD_BP234 Assembles to form an icosahedric capsid shell with a T=7 symmetry although with a diameter of about 82 nm, which is a larger volume than the usual T=7 capsids (PubMed:30737287). A dramatic reconfiguration of the capsid shell that expands the procaspid from a diameter of 66 nm to a supersized capsid of 82 nm, allows packaging of the large viral DNA genome (PubMed:30737287). The capsid decoration protein binds the expanded capsid and stabilizes it (PubMed:30737287).^[1]

Publication Abstract from PubMed

Double-stranded DNA viruses, including bacteriophages and herpesviruses, package their genomes into preformed capsids, using ATP-driven motors. Seeking to advance structural and mechanistic understanding, we established in vitro packaging for a thermostable bacteriophage, P23-45 of Thermus thermophilus Both the unexpanded procapsid and the expanded mature capsid can package DNA in the presence of packaging ATPase over the 20 degrees C to 70 degrees C temperature range, with optimum activity at 50 degrees C to 65 degrees C. Cryo-EM reconstructions for the mature and immature capsids at 3.7-A and 4.4-A resolution, respectively, reveal conformational changes during capsid expansion. Capsomer interactions in the expanded capsid are reinforced by formation of intersubunit beta-sheets with N-terminal segments of auxiliary protein trimers. Unexpectedly, the capsid has T=7 quasi-symmetry, despite the P23-45 genome being twice as large as those of known T=7 phages, in which the DNA is compacted to near-crystalline density. Our data explain this anomaly, showing how the canonical HK97 fold has adapted to double the volume of the capsid, while maintaining its structural integrity. Reconstructions of the procapsid and the expanded capsid defined the structure of the single vertex containing the portal protein. Together with a 1.95-A resolution crystal structure of the portal protein and DNA packaging assays, these reconstructions indicate that capsid expansion affects the conformation of the portal protein, while still allowing DNA to be packaged. These observations suggest a mechanism by which structural events inside the capsid can be communicated to the outside.

Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids.,Bayfield OW, Klimuk E, Winkler DC, Hesketh EL, Chechik M, Cheng N, Dykeman EC, Minakhin L, Ranson NA, Severinov K, Steven AC, Antson AA Proc Natl Acad Sci U S A. 2019 Feb 8. pii: 1813204116. doi:, 10.1073/pnas.1813204116. PMID:30737287^[2]

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

References

↑ Bayfield OW, Klimuk E, Winkler DC, Hesketh EL, Chechik M, Cheng N, Dykeman EC, Minakhin L, Ranson NA, Severinov K, Steven AC, Antson AA. Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids. Proc Natl Acad Sci U S A. 2019 Feb 8. pii: 1813204116. doi:, 10.1073/pnas.1813204116. PMID:30737287 doi:http://dx.doi.org/10.1073/pnas.1813204116
↑ Bayfield OW, Klimuk E, Winkler DC, Hesketh EL, Chechik M, Cheng N, Dykeman EC, Minakhin L, Ranson NA, Severinov K, Steven AC, Antson AA. Cryo-EM structure and in vitro DNA packaging of a thermophilic virus with supersized T=7 capsids. Proc Natl Acad Sci U S A. 2019 Feb 8. pii: 1813204116. doi:, 10.1073/pnas.1813204116. PMID:30737287 doi:http://dx.doi.org/10.1073/pnas.1813204116

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/6i9e"

@@ Line 3: / Line 3: @@
 <SX load='6i9e' size='340' side='right' viewer='molstar' caption='[[6i9e]], [[Resolution|resolution]] 3.74&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6i9e]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_virus_p23-45 Thermus virus p23-45]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I9E FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6i9e]] is a 14 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_virus_P23-45 Thermus virus P23-45]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6I9E OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6I9E FirstGlance]. <br>
-</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=6i9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i9e OCA], [https://pdbe.org/6i9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i9e RCSB], [https://www.ebi.ac.uk/pdbsum/6i9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i9e 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]] 3.74&#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=6i9e FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6i9e OCA], [https://pdbe.org/6i9e PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6i9e RCSB], [https://www.ebi.ac.uk/pdbsum/6i9e PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6i9e ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/CAPSD_BP234 CAPSD_BP234] Assembles to form an icosahedric capsid shell with a T=7 symmetry although with a diameter of about 82 nm, which is a larger volume than the usual T=7 capsids (PubMed:30737287). A dramatic reconfiguration of the capsid shell that expands the procaspid from a diameter of 66 nm to a supersized capsid of 82 nm, allows packaging of the large viral DNA genome (PubMed:30737287). The capsid decoration protein binds the expanded capsid and stabilizes it (PubMed:30737287).<ref>PMID:30737287</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 20: / Line 23: @@
 </SX>
 [[Category: Large Structures]]
-[[Category: Thermus virus p23-45]]
+[[Category: Thermus virus P23-45]]
-[[Category: Antson, A A]]
+[[Category: Antson AA]]
-[[Category: Bayfield, O W]]
+[[Category: Bayfield OW]]
-[[Category: Chechik, M]]
+[[Category: Chechik M]]
-[[Category: Cheng, N]]
+[[Category: Cheng N]]
-[[Category: Dykeman, E C]]
+[[Category: Dykeman EC]]
-[[Category: Hesketh, E L]]
+[[Category: Hesketh EL]]
-[[Category: Klimuk, E]]
+[[Category: Klimuk E]]
-[[Category: Minakhin, L]]
+[[Category: Minakhin L]]
-[[Category: Ranson, N A]]
+[[Category: Ranson NA]]
-[[Category: Severinov, K]]
+[[Category: Severinov K]]
-[[Category: Steven, A C]]
+[[Category: Steven AC]]
-[[Category: Winkler, D C]]
+[[Category: Winkler DC]]
-[[Category: Auxiliary]]
-[[Category: Bacteriophage]]
-[[Category: Capsid]]
-[[Category: Caudovirale]]
-[[Category: Hk97]]
-[[Category: Siphoviridae]]
-[[Category: Thermophage]]
-[[Category: Virus]]

6i9e

From Proteopedia

Current revision

Thermophage P23-45 empty expanded capsid

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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