1n7z - Revision history

OCA at 08:47, 10 April 2024

OCA — Wed, 10 Apr 2024 08:47:15 GMT

←Older revision		Revision as of 08:47, 10 April 2024
Line 3:		Line 3:
	<StructureSection load='1n7z' size='340' side='right'caption='[[1n7z]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1n7z' size='340' side='right'caption='[[1n7z]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1n7z]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpt4 Bpt4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1N7Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1n7z]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1N7Z FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 2Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;~~'>~~[[1n80\|1n80]]~~</~~div~~>~~</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=1n7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7z OCA], [https://pdbe.org/1n7z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1n7z RCSB], [https://www.ebi.ac.uk/pdbsum/1n7z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1n7z ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])~~</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=1n7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7z OCA], [~~http~~://pdbe.org/1n7z PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1n7z RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1n7z PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1n7z ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~VG08_BPT4 VG08_BPT4~~]~~] Structural component~~ of the baseplate.	+	[https://www.uniprot.org/uniprot/BP08_BPT4 BP08_BPT4] Baseplate protein that is part of the baseplate wedge. Involved in the tail assembly.<ref>PMID:15315755</ref> <ref>PMID:21129200</ref>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 22:		Line 20:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1n7z ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1n7z ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Many bacteriophages, such as T4, T7, RB49, and phi29, have complex, sometimes multilayered, tails that facilitate an almost 100% success rate for the viral particles to infect host cells. In bacteriophage T4, there is a baseplate, which is a multiprotein assembly, at the distal end of the contractile tail. The baseplate communicates to the tail that the phage fibers have attached to the host cell, thereby initiating the infection process. Gene product 8 (gp8), whose amino acid sequence consists of 334 residues, is one of at least 16 different structural proteins that constitute the T4 baseplate and is the sixth baseplate protein whose structure has been determined. A 2.0A resolution X-ray structure of gp8 shows that the two-domain protein forms a dimer, in which each monomer consists of a three-layered beta-sandwich with two loops, each containing an alpha-helix at the opposite sides of the sandwich. The crystals of gp8 were produced in the presence of concentrated chloride and bromide ions, resulting in at least 11 halide-binding sites per monomer. Five halide sites, situated at the N termini of alpha-helices, have a protein environment observed in other halide-containing protein crystal structures. The computer programs EMfit and SITUS were used to determine the positions of six gp8 dimers within the 12A resolution cryo-electron microscopy image reconstruction of the baseplate-tail tube complex. The gp8 dimers were found to be located in the upper part of the baseplate outer rim. About 20% of the gp8 surface is involved in contacts with other baseplate proteins, presumed to be gp6, gp7, and gp10. With the structure determination of gp8, a total of 53% of the volume of the baseplate has now been interpreted in terms of its atomic structure.
-
-	Structure and location of gene product 8 in the bacteriophage T4 baseplate.,Leiman PG, Shneider MM, Kostyuchenko VA, Chipman PR, Mesyanzhinov VV, Rossmann MG J Mol Biol. 2003 May 9;328(4):821-33. PMID:12729757<ref>PMID:12729757</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1n7z" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpt4~~]]	+	[[Category: Escherichia virus T4]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Chipman~~, P R~~]]	+	[[Category: Chipman PR]]
-	[[Category: Kostyuchenko~~, V A~~]]	+	[[Category: Kostyuchenko VA]]
-	[[Category: Leiman~~, P G~~]]	+	[[Category: Leiman PG]]
-	[[Category: Mesyanzhinov~~, V V~~]]	+	[[Category: Mesyanzhinov VV]]
-	[[Category: Rossmann~~, M G~~]]	+	[[Category: Rossmann MG]]
-	[[Category: Shneider~~, M M]]~~	+	[[Category: Shneider MM]]
-	~~[[Category: Bacteriophage t4]]~~	+
-	~~[[Category: Baseplate]]~~	+
-	~~[[Category: Beta sandwich]]~~	+
-	~~[[Category: Dimer]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 08:46, 2 December 2020

OCA — Wed, 02 Dec 2020 08:46:51 GMT

←Older revision		Revision as of 08:46, 2 December 2020
Line 1:		Line 1:

	==Structure and location of gene product 8 in the bacteriophage T4 baseplate==		==Structure and location of gene product 8 in the bacteriophage T4 baseplate==
-	<StructureSection load='1n7z' size='340' side='right' caption='[[1n7z]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1n7z' size='340' side='right'caption='[[1n7z]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1n7z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1N7Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1n7z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1N7Z FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n80\|1n80]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1n80\|1n80]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</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=1n7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7z OCA], [http://pdbe.org/1n7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n7z RCSB], [http://www.ebi.ac.uk/pdbsum/1n7z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n7z 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=1n7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7z OCA], [http://pdbe.org/1n7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n7z RCSB], [http://www.ebi.ac.uk/pdbsum/1n7z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n7z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 36:		Line 36:
	</StructureSection>		</StructureSection>
	[[Category: Bpt4]]		[[Category: Bpt4]]
		+	[[Category: Large Structures]]
	[[Category: Chipman, P R]]		[[Category: Chipman, P R]]
	[[Category: Kostyuchenko, V A]]		[[Category: Kostyuchenko, V A]]

OCA at 06:59, 7 February 2018

OCA — Wed, 07 Feb 2018 06:59:17 GMT

←Older revision		Revision as of 06:59, 7 February 2018
Line 1:		Line 1:
		+
	==Structure and location of gene product 8 in the bacteriophage T4 baseplate==		==Structure and location of gene product 8 in the bacteriophage T4 baseplate==
	<StructureSection load='1n7z' size='340' side='right' caption='[[1n7z]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1n7z' size='340' side='right' caption='[[1n7z]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n80\|1n80]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n80\|1n80]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</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=1n7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7z OCA], [http://pdbe.org/1n7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n7z RCSB], [http://www.ebi.ac.uk/pdbsum/1n7z 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=1n7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7z OCA], [http://pdbe.org/1n7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n7z RCSB], [http://www.ebi.ac.uk/pdbsum/1n7z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1n7z ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n7/1n7z_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n7/1n7z_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>

OCA at 22:47, 8 February 2016

OCA — Mon, 08 Feb 2016 22:47:03 GMT

←Older revision		Revision as of 22:47, 8 February 2016
Line 19:		Line 19:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1n7z ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 16:05, 10 September 2015

OCA — Thu, 10 Sep 2015 16:05:18 GMT

←Older revision		Revision as of 16:05, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1n7z' size='340' side='right' caption='[[1n7z]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1n7z' size='340' side='right' caption='[[1n7z]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1n7z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Enterobacteria_phage_t4 Enterobacteria phage t4~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N7Z FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1n7z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpt4 Bpt4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N7Z FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n80\|1n80]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n80\|1n80]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 ~~Enterobacteria phage T4~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 BPT4])</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=1n7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n7z RCSB], [http://www.ebi.ac.uk/pdbsum/1n7z 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=1n7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7z OCA], [http://pdbe.org/1n7z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1n7z RCSB], [http://www.ebi.ac.uk/pdbsum/1n7z PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1n7z" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Enterobacteria phage t4~~]]	+	[[Category: Bpt4]]
	[[Category: Chipman, P R]]		[[Category: Chipman, P R]]
	[[Category: Kostyuchenko, V A]]		[[Category: Kostyuchenko, V A]]

OCA at 02:38, 25 December 2014

OCA — Thu, 25 Dec 2014 02:38:54 GMT

←Older revision		Revision as of 02:38, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1n7z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N7Z FirstGlance]. <br>		<table><tr><td colspan='2'>[[1n7z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N7Z FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n80\|1n80]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n80\|1n80]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</td></tr>
-	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n7z RCSB], [http://www.ebi.ac.uk/pdbsum/1n7z 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=1n7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n7z RCSB], [http://www.ebi.ac.uk/pdbsum/1n7z PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/VG08_BPT4 VG08_BPT4]] Structural component of the baseplate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	</StructureSection>		</StructureSection>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
-	[[Category: Chipman, P R.]]	+	[[Category: Chipman, P R]]
-	[[Category: Kostyuchenko, V A.]]	+	[[Category: Kostyuchenko, V A]]
-	[[Category: Leiman, P G.]]	+	[[Category: Leiman, P G]]
-	[[Category: Mesyanzhinov, V V.]]	+	[[Category: Mesyanzhinov, V V]]
-	[[Category: Rossmann, M G.]]	+	[[Category: Rossmann, M G]]
-	[[Category: Shneider, M M.]]	+	[[Category: Shneider, M M]]
	[[Category: Bacteriophage t4]]		[[Category: Bacteriophage t4]]
	[[Category: Baseplate]]		[[Category: Baseplate]]

OCA at 13:02, 28 September 2014

OCA — Sun, 28 Sep 2014 13:02:52 GMT

←Older revision		Revision as of 13:02, 28 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1n7z.~~png~~\|~~left~~\|200px]]	+	==Structure and location of gene product 8 in the bacteriophage T4 baseplate==
		+	<StructureSection load='1n7z' size='340' side='right' caption='[[1n7z]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1n7z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1N7Z FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1n80\|1n80]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">gene 8 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10665 Enterobacteria phage T4])</td></tr>
		+	<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1n7z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1n7z OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1n7z RCSB], [http://www.ebi.ac.uk/pdbsum/1n7z PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n7/1n7z_consurf.spt"</scriptWhenChecked>
		+	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
		+	<text>to colour the structure by Evolutionary Conservation</text>
		+	</jmolCheckbox>
		+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Many bacteriophages, such as T4, T7, RB49, and phi29, have complex, sometimes multilayered, tails that facilitate an almost 100% success rate for the viral particles to infect host cells. In bacteriophage T4, there is a baseplate, which is a multiprotein assembly, at the distal end of the contractile tail. The baseplate communicates to the tail that the phage fibers have attached to the host cell, thereby initiating the infection process. Gene product 8 (gp8), whose amino acid sequence consists of 334 residues, is one of at least 16 different structural proteins that constitute the T4 baseplate and is the sixth baseplate protein whose structure has been determined. A 2.0A resolution X-ray structure of gp8 shows that the two-domain protein forms a dimer, in which each monomer consists of a three-layered beta-sandwich with two loops, each containing an alpha-helix at the opposite sides of the sandwich. The crystals of gp8 were produced in the presence of concentrated chloride and bromide ions, resulting in at least 11 halide-binding sites per monomer. Five halide sites, situated at the N termini of alpha-helices, have a protein environment observed in other halide-containing protein crystal structures. The computer programs EMfit and SITUS were used to determine the positions of six gp8 dimers within the 12A resolution cryo-electron microscopy image reconstruction of the baseplate-tail tube complex. The gp8 dimers were found to be located in the upper part of the baseplate outer rim. About 20% of the gp8 surface is involved in contacts with other baseplate proteins, presumed to be gp6, gp7, and gp10. With the structure determination of gp8, a total of 53% of the volume of the baseplate has now been interpreted in terms of its atomic structure.

-	~~{{STRUCTURE_1n7z\| PDB=1n7z \| SCENE= }}~~	+	Structure and location of gene product 8 in the bacteriophage T4 baseplate.,Leiman PG, Shneider MM, Kostyuchenko VA, Chipman PR, Mesyanzhinov VV, Rossmann MG J Mol Biol. 2003 May 9;328(4):821-33. PMID:12729757<ref>PMID:12729757</ref>

-	~~===Structure and location~~ of ~~gene product 8 in~~ the ~~bacteriophage T4 baseplate===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_12729757}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1n7z]] is a 4 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:012729757<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Chipman, P R.]]		[[Category: Chipman, P R.]]

OCA: Protected "1n7z" [edit=sysop:move=sysop]

OCA — Wed, 05 Dec 2012 19:31:37 GMT

Protected "1n7z" [edit=sysop:move=sysop]

←Older revision

Revision as of 19:31, 5 December 2012

OCA at 19:31, 5 December 2012

OCA — Wed, 05 Dec 2012 19:31:33 GMT

←Older revision		Revision as of 19:31, 5 December 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1n7z.png\|left\|200px]]		[[Image:1n7z.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1n7z", creates the "Structure Box" on the page.
-	You may change the PDB parameter (which sets the PDB file loaded into the applet)
-	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-	or leave the SCENE parameter empty for the default display.
-	-->
	{{STRUCTURE_1n7z\| PDB=1n7z \| SCENE= }}		{{STRUCTURE_1n7z\| PDB=1n7z \| SCENE= }}

	===Structure and location of gene product 8 in the bacteriophage T4 baseplate===		===Structure and location of gene product 8 in the bacteriophage T4 baseplate===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_12729757}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 12729757 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_12729757}}		{{ABSTRACT_PUBMED_12729757}}

	==About this Structure==		==About this Structure==
-	~~1N7Z~~ is a 4 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA].	+	[[1n7z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~12729757~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:012729757</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
	[[Category: Chipman, P R.]]		[[Category: Chipman, P R.]]
Line 35:		Line 23:
	[[Category: Beta sandwich]]		[[Category: Beta sandwich]]
	[[Category: Dimer]]		[[Category: Dimer]]
-		+	[[Category: Viral protein]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 04:08:22 2009''~~	+

OCA at 02:08, 17 February 2009

OCA — Tue, 17 Feb 2009 02:08:23 GMT

←Older revision		Revision as of 02:08, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1N7Z is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA].	+	1N7Z is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Enterobacteria_phage_t4 Enterobacteria phage t4]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1N7Z OCA].

	==Reference==		==Reference==
-	~~Structure and location of gene product 8 in the bacteriophage T4 baseplate., Leiman PG, Shneider MM, Kostyuchenko VA, Chipman PR, Mesyanzhinov VV, Rossmann MG, J Mol Biol. 2003 May 9;328(4):821-33.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/12729757 12729757]~~	+	<ref group="xtra">PMID:12729757</ref><references group="xtra"/>
	[[Category: Enterobacteria phage t4]]		[[Category: Enterobacteria phage t4]]
-	[[Category: Single protein]]
	[[Category: Chipman, P R.]]		[[Category: Chipman, P R.]]
	[[Category: Kostyuchenko, V A.]]		[[Category: Kostyuchenko, V A.]]
Line 37:		Line 36:
	[[Category: Dimer]]		[[Category: Dimer]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 07~~:32:~~13 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 04:08:22 2009''