6ibg

From Proteopedia

(Difference between revisions)

Current revision

Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus

Structural highlights

6ibg is a 3 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:	X-ray diffraction, Resolution 1.95Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PORTL_BP234 Forms the portal vertex of the capsid (By similarity). 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 (By similarity). Forms the portal vertex of the capsid. This portal plays critical roles in head assembly, genome packaging, neck/tail attachment, and genome ejection (By similarity).[UniProtKB:A0A1L4BKQ4]

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^[1]

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

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/6ibg"

@@ Line 3: / Line 3: @@
 <StructureSection load='6ibg' size='340' side='right'caption='[[6ibg]], [[Resolution|resolution]] 1.95&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6ibg]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Bp234 Bp234]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6IBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IBG FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6ibg]] is a 3 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=6IBG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6IBG FirstGlance]. <br>
-</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>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.95&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">P23p86 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=466051 BP234])</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=6ibg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ibg OCA], [https://pdbe.org/6ibg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ibg RCSB], [https://www.ebi.ac.uk/pdbsum/6ibg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ibg ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[https://www.uniprot.org/uniprot/PORTL_BP234 PORTL_BP234]] Forms the portal vertex of the capsid (By similarity). 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 (By similarity). Forms the portal vertex of the capsid. This portal plays critical roles in head assembly, genome packaging, neck/tail attachment, and genome ejection (By similarity).[UniProtKB:A0A1L4BKQ4]
+[https://www.uniprot.org/uniprot/PORTL_BP234 PORTL_BP234] Forms the portal vertex of the capsid (By similarity). 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 (By similarity). Forms the portal vertex of the capsid. This portal plays critical roles in head assembly, genome packaging, neck/tail attachment, and genome ejection (By similarity).[UniProtKB:A0A1L4BKQ4]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 21: @@
 ==See Also==
-*[[Portal protein|Portal protein]]
+*[[Portal protein 3D structures|Portal protein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bp234]]
 [[Category: Large Structures]]
-[[Category: Antson, A A]]
+[[Category: Thermus virus P23-45]]
-[[Category: Bayfield, O W]]
+[[Category: Antson AA]]
-[[Category: Chechik, M]]
+[[Category: Bayfield OW]]
-[[Category: Cheng, N]]
+[[Category: Chechik M]]
-[[Category: Dykeman, E C]]
+[[Category: Cheng N]]
-[[Category: Hesketh, E L]]
+[[Category: Dykeman EC]]
-[[Category: Klimuk, E]]
+[[Category: Hesketh EL]]
-[[Category: Minakhin, L]]
+[[Category: Klimuk E]]
-[[Category: Ranson, N A]]
+[[Category: Minakhin L]]
-[[Category: Severinov, K]]
+[[Category: Ranson NA]]
-[[Category: Steven, A C]]
+[[Category: Severinov K]]
-[[Category: Winkler, D C]]
+[[Category: Steven AC]]
-[[Category: Auxiliary]]
+[[Category: Winkler DC]]
-[[Category: Bacteriophage]]
-[[Category: Capsid]]
-[[Category: Caudovirale]]
-[[Category: Hk97]]
-[[Category: Siphoviridae]]
-[[Category: Thermophage]]
-[[Category: Viral protein]]
-[[Category: Virus]]

6ibg

From Proteopedia

Current revision

Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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