5fei - Revision history

OCA at 09:12, 20 March 2024

OCA — Wed, 20 Mar 2024 09:12:01 GMT

←Older revision		Revision as of 09:12, 20 March 2024
Line 10:		Line 10:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/DIT9_BPPH2 DIT9_BPPH2] Forms the distal part (knob) of the tail tube.<ref>PMID:18606992</ref>		[https://www.uniprot.org/uniprot/DIT9_BPPH2 DIT9_BPPH2] Forms the distal part (knob) of the tail tube.<ref>PMID:18606992</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Most bacteriophages are tailed bacteriophages with an isometric or a prolate head attached to a long contractile, long non-contractile, or short non-contractile tail. The tail is a complex machine that plays a central role in host cell recognition and attachment, cell wall and membrane penetration, and viral genome ejection. The mechanisms involved in the penetration of the inner host cell membrane by bacteriophage tails are not well understood. Here we describe structural and functional studies of the bacteriophage varphi29 tail knob protein gene product 9 (gp9). The 2.0 A crystal structure of gp9 shows that six gp9 molecules form a hexameric tube structure with six flexible hydrophobic loops blocking one end of the tube before DNA ejection. Sequence and structural analyses suggest that the loops in the tube could be membrane active. Further biochemical assays and electron microscopy structural analyses show that the six hydrophobic loops in the tube exit upon DNA ejection and form a channel that spans the lipid bilayer of the membrane and allows the release of the bacteriophage genomic DNA, suggesting that cell membrane penetration involves a pore-forming mechanism similar to that of certain non-enveloped eukaryotic viruses. A search of other phage tail proteins identified similar hydrophobic loops, which indicates that a common mechanism might be used for membrane penetration by prokaryotic viruses. These findings suggest that although prokaryotic and eukaryotic viruses use apparently very different mechanisms for infection, they have evolved similar mechanisms for breaching the cell membrane.
-
-	The bacteriophage varphi29 tail possesses a pore-forming loop for cell membrane penetration.,Xu J, Gui M, Wang D, Xiang Y Nature. 2016 Jun 15;534(7608):544-7. doi: 10.1038/nature18017. PMID:27309813<ref>PMID:27309813</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5fei" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:48, 19 July 2023

OCA — Wed, 19 Jul 2023 06:48:17 GMT

←Older revision		Revision as of 06:48, 19 July 2023
Line 3:		Line 3:
	<StructureSection load='5fei' size='340' side='right'caption='[[5fei]], [[Resolution\|resolution]] 2.60Å' scene=''>		<StructureSection load='5fei' size='340' side='right'caption='[[5fei]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fei]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpph2 Bpph2~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FEI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5FEI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fei]] is a 2 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=5FEI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5FEI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.604Å</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=5fei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fei OCA], [~~http~~://pdbe.org/5fei PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5fei RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5fei PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5fei ProSAT]</span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5fei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fei OCA], [https://pdbe.org/5fei PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5fei RCSB], [https://www.ebi.ac.uk/pdbsum/5fei PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5fei ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DIT9_BPPH2 DIT9_BPPH2]] Forms the distal part (knob) of the tail tube.<ref>PMID:18606992</ref>	+	[https://www.uniprot.org/uniprot/DIT9_BPPH2 DIT9_BPPH2] Forms the distal part (knob) of the tail tube.<ref>PMID:18606992</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 22:		Line 23:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpph2~~]]	+	[[Category: Bacillus virus phi29]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Gui, M]]	+	[[Category: Gui M]]
-	[[Category: Wang~~, D H~~]]	+	[[Category: Wang DH]]
-	[[Category: Xiang, Y]]	+	[[Category: Xiang Y]]
-	[[Category: Xu~~, J W]]~~	+	[[Category: Xu JW]]
-	~~[[Category: Bacteriophage phi29]]~~	+
-	~~[[Category: Tail knob]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 07:15, 6 May 2020

OCA — Wed, 06 May 2020 07:15:20 GMT

←Older revision		Revision as of 07:15, 6 May 2020
Line 1:		Line 1:

	==Crystal structure of the bacteriophage phi29 tail knob protein gp9 truncation variant==		==Crystal structure of the bacteriophage phi29 tail knob protein gp9 truncation variant==
-	<StructureSection load='5fei' size='340' side='right' caption='[[5fei]], [[Resolution\|resolution]] 2.60Å' scene=''>	+	<StructureSection load='5fei' size='340' side='right'caption='[[5fei]], [[Resolution\|resolution]] 2.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5fei]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FEI OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5FEI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5fei]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpph2 Bpph2]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FEI OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5FEI FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5fei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fei OCA], [http://pdbe.org/5fei PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fei RCSB], [http://www.ebi.ac.uk/pdbsum/5fei PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fei ProSAT]</span></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=5fei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fei OCA], [http://pdbe.org/5fei PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fei RCSB], [http://www.ebi.ac.uk/pdbsum/5fei PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fei ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 22:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpph2]]
		+	[[Category: Large Structures]]
	[[Category: Gui, M]]		[[Category: Gui, M]]
	[[Category: Wang, D H]]		[[Category: Wang, D H]]

OCA at 17:47, 12 July 2016

OCA — Tue, 12 Jul 2016 17:47:31 GMT

←Older revision		Revision as of 17:47, 12 July 2016
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[5fei]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FEI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FEI FirstGlance]. <br>		<table><tr><td colspan='2'>[[5fei]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FEI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FEI FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5fei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fei OCA], [http://pdbe.org/5fei PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fei RCSB], [http://www.ebi.ac.uk/pdbsum/5fei PDBsum]</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=5fei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fei OCA], [http://pdbe.org/5fei PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fei RCSB], [http://www.ebi.ac.uk/pdbsum/5fei PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5fei ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/DIT9_BPPH2 DIT9_BPPH2]] Forms the distal part (knob) of the tail tube.<ref>PMID:18606992</ref>		[[http://www.uniprot.org/uniprot/DIT9_BPPH2 DIT9_BPPH2]] Forms the distal part (knob) of the tail tube.<ref>PMID:18606992</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Most bacteriophages are tailed bacteriophages with an isometric or a prolate head attached to a long contractile, long non-contractile, or short non-contractile tail. The tail is a complex machine that plays a central role in host cell recognition and attachment, cell wall and membrane penetration, and viral genome ejection. The mechanisms involved in the penetration of the inner host cell membrane by bacteriophage tails are not well understood. Here we describe structural and functional studies of the bacteriophage varphi29 tail knob protein gene product 9 (gp9). The 2.0 A crystal structure of gp9 shows that six gp9 molecules form a hexameric tube structure with six flexible hydrophobic loops blocking one end of the tube before DNA ejection. Sequence and structural analyses suggest that the loops in the tube could be membrane active. Further biochemical assays and electron microscopy structural analyses show that the six hydrophobic loops in the tube exit upon DNA ejection and form a channel that spans the lipid bilayer of the membrane and allows the release of the bacteriophage genomic DNA, suggesting that cell membrane penetration involves a pore-forming mechanism similar to that of certain non-enveloped eukaryotic viruses. A search of other phage tail proteins identified similar hydrophobic loops, which indicates that a common mechanism might be used for membrane penetration by prokaryotic viruses. These findings suggest that although prokaryotic and eukaryotic viruses use apparently very different mechanisms for infection, they have evolved similar mechanisms for breaching the cell membrane.
		+
		+	The bacteriophage varphi29 tail possesses a pore-forming loop for cell membrane penetration.,Xu J, Gui M, Wang D, Xiang Y Nature. 2016 Jun 15;534(7608):544-7. doi: 10.1038/nature18017. PMID:27309813<ref>PMID:27309813</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5fei" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 23:26, 23 June 2016

OCA — Thu, 23 Jun 2016 23:26:28 GMT

←Older revision		Revision as of 23:26, 23 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 5fei is ON HOLD until Paper Publication~~	+	==Crystal structure of the bacteriophage phi29 tail knob protein gp9 truncation variant==
-		+	<StructureSection load='5fei' size='340' side='right' caption='[[5fei]], [[Resolution\|resolution]] 2.60Å' scene=''>
-	~~Authors: Xu, J.W., Gui, M., Wang, D.H., Xiang, Y.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5fei]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5FEI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5FEI FirstGlance]. <br>
-	~~Description:~~ Crystal structure of the bacteriophage phi29 tail knob protein gp9 truncation variant	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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=5fei FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5fei OCA], [http://pdbe.org/5fei PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5fei RCSB], [http://www.ebi.ac.uk/pdbsum/5fei PDBsum]</span></td></tr>
-	[[~~Category~~: ~~Wang~~, D.H]]	+	</table>
-	[[~~Category~~: ~~Xu, J~~.W]]	+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DIT9_BPPH2 DIT9_BPPH2]] Forms the distal part (knob) of the tail tube.<ref>PMID:18606992</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Gui, M]]		[[Category: Gui, M]]
		+	[[Category: Wang, D H]]
	[[Category: Xiang, Y]]		[[Category: Xiang, Y]]
		+	[[Category: Xu, J W]]
		+	[[Category: Bacteriophage phi29]]
		+	[[Category: Tail knob]]
		+	[[Category: Viral protein]]

OCA at 22:53, 10 May 2016

OCA — Tue, 10 May 2016 22:53:14 GMT

←Older revision		Revision as of 22:53, 10 May 2016
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5fei is ON HOLD	+	The entry 5fei is ON HOLD until Paper Publication

	Authors: Xu, J.W., Gui, M., Wang, D.H., Xiang, Y.		Authors: Xu, J.W., Gui, M., Wang, D.H., Xiang, Y.

OCA at 12:57, 3 February 2016

OCA — Wed, 03 Feb 2016 12:57:51 GMT

←Older revision		Revision as of 12:57, 3 February 2016
Line 5:		Line 5:
	Authors: Xu, J.W., Gui, M., Wang, D.H., Xiang, Y.		Authors: Xu, J.W., Gui, M., Wang, D.H., Xiang, Y.

-	Description: ~~Bacteriophage~~ phi29 tail knob protein gp9 truncation	+	Description: Crystal structure of the bacteriophage phi29 tail knob protein gp9 truncation variant
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
	[[Category: Wang, D.H]]		[[Category: Wang, D.H]]

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

OCA — Wed, 23 Dec 2015 11:33:03 GMT

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

←Older revision

Revision as of 11:33, 23 December 2015

OCA: New page: '''Unreleased structure''' The entry 5fei is ON HOLD Authors: Xu, J.W., Gui, M., Wang, D.H., Xiang, Y. Description: Bacteriophage phi29 tail knob protein gp9 truncation [[Category: Unr...

OCA — Wed, 23 Dec 2015 11:33:02 GMT

New page: '''Unreleased structure''' The entry 5fei is ON HOLD Authors: Xu, J.W., Gui, M., Wang, D.H., Xiang, Y. Description: Bacteriophage phi29 tail knob protein gp9 truncation [[Category: Unr...

New page

'''Unreleased structure'''

The entry 5fei is ON HOLD

Authors: Xu, J.W., Gui, M., Wang, D.H., Xiang, Y.

Description: Bacteriophage phi29 tail knob protein gp9 truncation
[[Category: Unreleased Structures]]
[[Category: Wang, D.H]]
[[Category: Xu, J.W]]
[[Category: Gui, M]]
[[Category: Xiang, Y]]