5yvq - Revision history

OCA at 10:25, 27 March 2024

OCA — Wed, 27 Mar 2024 10:25:24 GMT

←Older revision		Revision as of 10:25, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5yvq' size='340' side='right'caption='[[5yvq]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5yvq' size='340' side='right'caption='[[5yvq]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yvq]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpmu Bpmu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YVQ OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5YVQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yvq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_Mu Escherichia virus Mu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YVQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YVQ FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</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]] 2.103Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~S, Mup49 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=10677 BPMU]), U, Mup50 ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10677 BPMU])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></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=5yvq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvq OCA], [~~http~~://pdbe.org/5yvq PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5yvq RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5yvq PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvq 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=5yvq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvq OCA], [https://pdbe.org/5yvq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5yvq RCSB], [https://www.ebi.ac.uk/pdbsum/5yvq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/S1_BPMU S1_BPMU]] Component of the tail fiber that acts as receptor binding protein. Binds to the primary receptor, thereby determining the host range. Two alternate tail fiber S and S' proteins are encoded extending the host range of the virus.<ref>PMID:6250048</ref> [[http://www.uniprot.org/uniprot/U1_BPMU U1_BPMU]] Chaperone involved in tail fiber assembly. Remains associated to the tail fiber and participates in the host receptor binding. Binds to the primary receptor (Probable). Two alternate tail fiber assembly proteins U and U' are encoded extending the host range of the virus.	+	[https://www.uniprot.org/uniprot/S1_BPMU S1_BPMU] Component of the tail fiber that acts as receptor binding protein. Binds to the primary receptor, thereby determining the host range. Two alternate tail fiber S and S' proteins are encoded extending the host range of the virus.<ref>PMID:6250048</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Phage tail fibres are elongated protein assemblies capable of specific recognition of bacterial surfaces during the first step of viral infection(1-4). The folding of these complex trimeric structures often requires a phage-encoded tail fibre assembly (Tfa) protein(5-7). Despite the wide occurrence of Tfa proteins, their functional mechanism has not been elucidated. Here, we investigate the tail fibre and Tfa of Escherichia coli phage Mu. We demonstrate that Tfa forms a stable complex with the tail fibre, and present a 2.1 A resolution X-ray crystal structure of this complex. We find that Tfa proteins are comprised of two domains: a non-conserved N-terminal domain that binds to the C-terminal region of the fibre and a conserved C-terminal domain that probably mediates fibre oligomerization and assembly. Tfa forms rapidly exchanging multimers on its own, but not a stable trimer, implying that Tfa does not specify the trimeric state of the fibre. We propose that the key conserved role of Tfa is to ensure that fibre assembly and multimerization initiates at the C terminus, ensuring that the intertwined and repetitive structural elements of fibres come together in the correct sequence. The universal importance of correctly aligning the C termini of phage fibres is highlighted by our work.	+
-		+
-	Phage tail fibre assembly proteins employ a modular structure to drive the correct folding of diverse fibres.,North OI, Sakai K, Yamashita E, Nakagawa A, Iwazaki T, Buttner CR, Takeda S, Davidson AR Nat Microbiol. 2019 Oct;4(10):1645-1653. doi: 10.1038/s41564-019-0477-7. Epub, 2019 Jun 17. PMID:31209305<ref>PMID:31209305</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5yvq" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpmu~~]]	+	[[Category: Escherichia virus Mu]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Iwazaki, T]]	+	[[Category: Iwazaki T]]
-	[[Category: Nakagawa, A]]	+	[[Category: Nakagawa A]]
-	[[Category: Sakai, K]]	+	[[Category: Sakai K]]
-	[[Category: Takeda, S]]	+	[[Category: Takeda S]]
-	[[Category: Yamashita, E]]	+	[[Category: Yamashita E]]
-	~~[[Category: Bacteriophage]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 05:58, 10 October 2019

OCA — Thu, 10 Oct 2019 05:58:33 GMT

←Older revision		Revision as of 05:58, 10 October 2019
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	<StructureSection load='5yvq' size='340' side='right'caption='[[5yvq]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='5yvq' size='340' side='right'caption='[[5yvq]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5yvq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YVQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YVQ FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5yvq]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpmu Bpmu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YVQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YVQ FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">S, Mup49 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10677 BPMU]), U, Mup50 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10677 BPMU])</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=5yvq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvq OCA], [http://pdbe.org/5yvq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yvq RCSB], [http://www.ebi.ac.uk/pdbsum/5yvq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvq 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=5yvq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvq OCA], [http://pdbe.org/5yvq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yvq RCSB], [http://www.ebi.ac.uk/pdbsum/5yvq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvq ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/S1_BPMU S1_BPMU]] Component of the tail fiber that acts as receptor binding protein. Binds to the primary receptor, thereby determining the host range. Two alternate tail fiber S and S' proteins are encoded extending the host range of the virus.<ref>PMID:6250048</ref> [[http://www.uniprot.org/uniprot/U1_BPMU U1_BPMU]] Chaperone involved in tail fiber assembly. Remains associated to the tail fiber and participates in the host receptor binding. Binds to the primary receptor (Probable). Two alternate tail fiber assembly proteins U and U' are encoded extending the host range of the virus.		[[http://www.uniprot.org/uniprot/S1_BPMU S1_BPMU]] Component of the tail fiber that acts as receptor binding protein. Binds to the primary receptor, thereby determining the host range. Two alternate tail fiber S and S' proteins are encoded extending the host range of the virus.<ref>PMID:6250048</ref> [[http://www.uniprot.org/uniprot/U1_BPMU U1_BPMU]] Chaperone involved in tail fiber assembly. Remains associated to the tail fiber and participates in the host receptor binding. Binds to the primary receptor (Probable). Two alternate tail fiber assembly proteins U and U' are encoded extending the host range of the virus.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Phage tail fibres are elongated protein assemblies capable of specific recognition of bacterial surfaces during the first step of viral infection(1-4). The folding of these complex trimeric structures often requires a phage-encoded tail fibre assembly (Tfa) protein(5-7). Despite the wide occurrence of Tfa proteins, their functional mechanism has not been elucidated. Here, we investigate the tail fibre and Tfa of Escherichia coli phage Mu. We demonstrate that Tfa forms a stable complex with the tail fibre, and present a 2.1 A resolution X-ray crystal structure of this complex. We find that Tfa proteins are comprised of two domains: a non-conserved N-terminal domain that binds to the C-terminal region of the fibre and a conserved C-terminal domain that probably mediates fibre oligomerization and assembly. Tfa forms rapidly exchanging multimers on its own, but not a stable trimer, implying that Tfa does not specify the trimeric state of the fibre. We propose that the key conserved role of Tfa is to ensure that fibre assembly and multimerization initiates at the C terminus, ensuring that the intertwined and repetitive structural elements of fibres come together in the correct sequence. The universal importance of correctly aligning the C termini of phage fibres is highlighted by our work.
		+
		+	Phage tail fibre assembly proteins employ a modular structure to drive the correct folding of diverse fibres.,North OI, Sakai K, Yamashita E, Nakagawa A, Iwazaki T, Buttner CR, Takeda S, Davidson AR Nat Microbiol. 2019 Oct;4(10):1645-1653. doi: 10.1038/s41564-019-0477-7. Epub, 2019 Jun 17. PMID:31209305<ref>PMID:31209305</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5yvq" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpmu]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Iwazaki, T]]		[[Category: Iwazaki, T]]

OCA at 06:40, 23 May 2019

OCA — Thu, 23 May 2019 06:40:18 GMT

←Older revision		Revision as of 06:40, 23 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5yvq is ~~ON HOLD until May 21 2020~~	+	==Complex of Mu phage tail fiber and its chaperone==
-		+	<StructureSection load='5yvq' size='340' side='right'caption='[[5yvq]], [[Resolution\|resolution]] 2.10Å' scene=''>
-	~~Authors~~: ~~Takeda~~, S., ~~Sakai, K~~., ~~Iwazaki, T~~., ~~Yamashita, E~~., ~~Nakagawa, A~~.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5yvq]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YVQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YVQ FirstGlance]. <br>
-	~~Description~~: ~~Complex~~ of ~~Mu phage~~ tail fiber and ~~its chaperone~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=5yvq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5yvq OCA], [http://pdbe.org/5yvq PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5yvq RCSB], [http://www.ebi.ac.uk/pdbsum/5yvq PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5yvq ProSAT]</span></td></tr>
-	[[Category: ~~Yamashita~~, E]]	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/S1_BPMU S1_BPMU]] Component of the tail fiber that acts as receptor binding protein. Binds to the primary receptor, thereby determining the host range. Two alternate tail fiber S and S' proteins are encoded extending the host range of the virus.<ref>PMID:6250048</ref> [[http://www.uniprot.org/uniprot/U1_BPMU U1_BPMU]] Chaperone involved in tail fiber assembly. Remains associated to the tail fiber and participates in the host receptor binding. Binds to the primary receptor (Probable). Two alternate tail fiber assembly proteins U and U' are encoded extending the host range of the virus.
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Iwazaki, T]]
		+	[[Category: Nakagawa, A]]
	[[Category: Sakai, K]]		[[Category: Sakai, K]]
-	[[Category: Iwazaki, T]]
	[[Category: Takeda, S]]		[[Category: Takeda, S]]
-	[[Category: ~~Nakagawa~~, A]]	+	[[Category: Yamashita, E]]
		+	[[Category: Bacteriophage]]
		+	[[Category: Viral protein]]

OCA at 05:33, 21 May 2019

OCA — Tue, 21 May 2019 05:33:27 GMT

←Older revision		Revision as of 05:33, 21 May 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5yvq is ON HOLD	+	The entry 5yvq is ON HOLD until May 21 2020

	Authors: Takeda, S., Sakai, K., Iwazaki, T., Yamashita, E., Nakagawa, A.		Authors: Takeda, S., Sakai, K., Iwazaki, T., Yamashita, E., Nakagawa, A.
Line 9:		Line 9:
	[[Category: Yamashita, E]]		[[Category: Yamashita, E]]
	[[Category: Sakai, K]]		[[Category: Sakai, K]]
-	[[Category: Takeda, S]]
	[[Category: Iwazaki, T]]		[[Category: Iwazaki, T]]
		+	[[Category: Takeda, S]]
	[[Category: Nakagawa, A]]		[[Category: Nakagawa, A]]

OCA at 06:49, 1 May 2019

OCA — Wed, 01 May 2019 06:49:16 GMT

←Older revision		Revision as of 06:49, 1 May 2019
Line 3:		Line 3:
	The entry 5yvq is ON HOLD		The entry 5yvq is ON HOLD

-	Authors: Takeda, S., Sakai, K., ~~Iwasaki~~, T., Yamashita, E., Nakagawa, A.	+	Authors: Takeda, S., Sakai, K., Iwazaki, T., Yamashita, E., Nakagawa, A.

	Description: Complex of Mu phage tail fiber and its chaperone		Description: Complex of Mu phage tail fiber and its chaperone
Line 10:		Line 10:
	[[Category: Sakai, K]]		[[Category: Sakai, K]]
	[[Category: Takeda, S]]		[[Category: Takeda, S]]
-	[[Category: ~~Iwasaki~~, T]]	+	[[Category: Iwazaki, T]]
	[[Category: Nakagawa, A]]		[[Category: Nakagawa, A]]

OCA: Protected "5yvq" [edit=sysop:move=sysop]

OCA — Wed, 06 Dec 2017 05:58:48 GMT

Protected "5yvq" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:58, 6 December 2017

OCA: New page: '''Unreleased structure''' The entry 5yvq is ON HOLD Authors: Takeda, S., Sakai, K., Iwasaki, T., Yamashita, E., Nakagawa, A. Description: Complex of Mu phage tail fiber and its chaper...

OCA — Wed, 06 Dec 2017 05:58:47 GMT

New page: '''Unreleased structure''' The entry 5yvq is ON HOLD Authors: Takeda, S., Sakai, K., Iwasaki, T., Yamashita, E., Nakagawa, A. Description: Complex of Mu phage tail fiber and its chaper...

New page

'''Unreleased structure'''

The entry 5yvq is ON HOLD

Authors: Takeda, S., Sakai, K., Iwasaki, T., Yamashita, E., Nakagawa, A.

Description: Complex of Mu phage tail fiber and its chaperone
[[Category: Unreleased Structures]]
[[Category: Yamashita, E]]
[[Category: Sakai, K]]
[[Category: Takeda, S]]
[[Category: Iwasaki, T]]
[[Category: Nakagawa, A]]