6ibg - Revision history

OCA at 11:04, 30 March 2022

OCA — Wed, 30 Mar 2022 11:04:04 GMT

←Older revision		Revision as of 11:04, 30 March 2022
Line 3:		Line 3:
	<StructureSection load='6ibg' size='340' side='right'caption='[[6ibg]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='6ibg' size='340' side='right'caption='[[6ibg]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ibg]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpg20 Bpg20~~]. 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 [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/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/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>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>	+	</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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">P23p86 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~1406341 BPG20~~])</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6ibg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ibg OCA], [~~http~~://pdbe.org/6ibg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ibg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ibg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ibg ProSAT]</span></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>		</table>
	== Function ==		== Function ==
-	[[~~http~~://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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 6ibg" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6ibg" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Portal protein\|Portal protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpg20~~]]	+	[[Category: Bp234]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Antson, A A]]		[[Category: Antson, A A]]

OCA at 09:31, 30 October 2019

OCA — Wed, 30 Oct 2019 09:31:29 GMT

←Older revision		Revision as of 09:31, 30 October 2019
Line 1:		Line 1:

	==Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus==		==Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus==
-	<StructureSection load='6ibg' size='340' side='right' caption='[[6ibg]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='6ibg' size='340' side='right'caption='[[6ibg]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ibg]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_phage_g20c Thermus phage g20c~~]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IBG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ibg]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpg20 Bpg20]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IBG FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">~~G20c_81~~ ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1406341 ~~Thermus phage G20c~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">P23p86 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1406341 BPG20])</td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ibg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ibg OCA], [http://pdbe.org/6ibg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ibg RCSB], [http://www.ebi.ac.uk/pdbsum/6ibg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ibg ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ibg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ibg OCA], [http://pdbe.org/6ibg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ibg RCSB], [http://www.ebi.ac.uk/pdbsum/6ibg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ibg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://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;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus phage g20c~~]]	+	[[Category: Bpg20]]
		+	[[Category: Large Structures]]
	[[Category: Antson, A A]]		[[Category: Antson, A A]]
	[[Category: Bayfield, O W]]		[[Category: Bayfield, O W]]

OCA at 08:28, 6 March 2019

OCA — Wed, 06 Mar 2019 08:28:10 GMT

←Older revision		Revision as of 08:28, 6 March 2019
Line 1:		Line 1:

	==Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus==		==Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus==
-	<StructureSection load='6ibg' size='340' side='right' caption='[[6ibg]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='6ibg' size='340' side='right' caption='[[6ibg]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6ibg]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_phage_g20c Thermus phage g20c]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IBG FirstGlance]. <br>		<table><tr><td colspan='2'>[[6ibg]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_phage_g20c Thermus phage g20c]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IBG FirstGlance]. <br>

OCA at 16:01, 27 February 2019

OCA — Wed, 27 Feb 2019 16:01:22 GMT

←Older revision		Revision as of 16:01, 27 February 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ibg is ~~ON HOLD~~	+	==Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus==
		+	<StructureSection load='6ibg' size='340' side='right' caption='[[6ibg]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6ibg]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_phage_g20c Thermus phage g20c]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6IBG FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">G20c_81 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1406341 Thermus phage G20c])</td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6ibg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ibg OCA], [http://pdbe.org/6ibg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ibg RCSB], [http://www.ebi.ac.uk/pdbsum/6ibg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ibg ProSAT]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== 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.

-	~~Authors:~~ Bayfield~~, O.W.~~, Klimuk, E., Winkler~~, D.C.~~, Hesketh~~, E.L.~~, Chechik, M., Cheng, N., Dykeman~~, E.C.~~, Minakhin, L., Ranson~~, N.A.~~, Severinov, K., Steven, A.C., ~~Antson, A~~.A.	+	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<ref>PMID:30737287</ref>

-	~~Description: Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Klimuk, E]]~~	+	<div class="pdbe-citations 6ibg" style="background-color:#fffaf0;"></div>
-	~~[[Category: Bayfield, O.W]]~~	+	== References ==
-	~~[[Category: Steven, A.C]]~~	+	<references/>
-	[[Category: ~~Hesketh, E.L~~]]	+	__TOC__
-	[[Category: ~~Winkler~~, ~~D.C~~]]	+	</StructureSection>
-	[[Category: ~~Antson~~, ~~A.A~~]]	+	[[Category: Thermus phage g20c]]
		+	[[Category: Antson, A A]]
		+	[[Category: Bayfield, O W]]
	[[Category: Chechik, M]]		[[Category: Chechik, M]]
-	[[Category: Severinov, K]]
-	[[Category: Minakhin, L]]
-	[[Category: Dykeman, E.C]]
-	[[Category: Ranson, N.A]]
	[[Category: Cheng, N]]		[[Category: Cheng, N]]
		+	[[Category: Dykeman, E C]]
		+	[[Category: Hesketh, E L]]
		+	[[Category: Klimuk, E]]
		+	[[Category: Minakhin, L]]
		+	[[Category: Ranson, N A]]
		+	[[Category: Severinov, K]]
		+	[[Category: Steven, A C]]
		+	[[Category: Winkler, D C]]
		+	[[Category: Auxiliary]]
		+	[[Category: Bacteriophage]]
		+	[[Category: Capsid]]
		+	[[Category: Caudovirale]]
		+	[[Category: Hk97]]
		+	[[Category: Siphoviridae]]
		+	[[Category: Thermophage]]
		+	[[Category: Viral protein]]
		+	[[Category: Virus]]

OCA: Protected "6ibg" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2018 05:05:49 GMT

Protected "6ibg" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:05, 5 December 2018

OCA: New page: '''Unreleased structure''' The entry 6ibg is ON HOLD Authors: Bayfield, O.W., Klimuk, E., Winkler, D.C., Hesketh, E.L., Chechik, M., Cheng, N., Dykeman, E.C., Minakhin, L., Ranson, N.A....

OCA — Wed, 05 Dec 2018 05:05:47 GMT

New page: '''Unreleased structure''' The entry 6ibg is ON HOLD Authors: Bayfield, O.W., Klimuk, E., Winkler, D.C., Hesketh, E.L., Chechik, M., Cheng, N., Dykeman, E.C., Minakhin, L., Ranson, N.A....

New page

'''Unreleased structure'''

The entry 6ibg is ON HOLD

Authors: Bayfield, O.W., Klimuk, E., Winkler, D.C., Hesketh, E.L., Chechik, M., Cheng, N., Dykeman, E.C., Minakhin, L., Ranson, N.A., Severinov, K., Steven, A.C., Antson, A.A.

Description: Bacteriophage G20c portal protein crystal structure for construct with intact N-terminus
[[Category: Unreleased Structures]]
[[Category: Klimuk, E]]
[[Category: Bayfield, O.W]]
[[Category: Steven, A.C]]
[[Category: Hesketh, E.L]]
[[Category: Winkler, D.C]]
[[Category: Antson, A.A]]
[[Category: Chechik, M]]
[[Category: Severinov, K]]
[[Category: Minakhin, L]]
[[Category: Dykeman, E.C]]
[[Category: Ranson, N.A]]
[[Category: Cheng, N]]