6yeg - Revision history

OCA at 16:03, 14 March 2024

OCA — Thu, 14 Mar 2024 16:03:26 GMT

←Older revision		Revision as of 16:03, 14 March 2024
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[6yeg]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_phage_SPP1 Bacillus phage SPP1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YEG FirstGlance]. <br>		<table><tr><td colspan='2'>[[6yeg]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_phage_SPP1 Bacillus phage SPP1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YEG FirstGlance]. <br>
-	</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=6yeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yeg OCA], [https://pdbe.org/6yeg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yeg RCSB], [https://www.ebi.ac.uk/pdbsum/6yeg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yeg ProSAT]</span></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy , Hybrid , Solid-state NMR, [[Resolution\|Resolution]] 4Å</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=6yeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yeg OCA], [https://pdbe.org/6yeg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yeg RCSB], [https://www.ebi.ac.uk/pdbsum/6yeg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yeg ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/TUBE_BPSPP TUBE_BPSPP] Forms the 160 nm long, sixfold helical, rigid tail tube. Binding to the entry receptor triggers structural rearrangements of the tail tube leading to ejection of the phage DNA into the host.<ref>PMID:17611601</ref> <ref>PMID:18786146</ref> <ref>PMID:25525268</ref> <ref>PMID:25991862</ref>		[https://www.uniprot.org/uniprot/TUBE_BPSPP TUBE_BPSPP] Forms the 160 nm long, sixfold helical, rigid tail tube. Binding to the entry receptor triggers structural rearrangements of the tail tube leading to ejection of the phage DNA into the host.<ref>PMID:17611601</ref> <ref>PMID:18786146</ref> <ref>PMID:25525268</ref> <ref>PMID:25991862</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Bacteriophage SPP1 is a double-stranded DNA virus of the Siphoviridae family that infects the bacterium Bacillus subtilis. This family of phages features a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, we present the atomic structure of the tail tube of phage SPP1. Our hybrid structure is based on the integration of structural restraints from solid-state nuclear magnetic resonance (NMR) and a density map from cryo-EM. We show that the tail tube protein gp17.1 organizes into hexameric rings that are stacked by flexible linker domains and, thus, form a hollow flexible tube with a negatively charged lumen suitable for the transport of DNA. Additionally, we assess the dynamics of the system by combining relaxation measurements with variances in density maps.
-
-	Architecture of the flexible tail tube of bacteriophage SPP1.,Zinke M, Sachowsky KAA, Oster C, Zinn-Justin S, Ravelli R, Schroder GF, Habeck M, Lange A Nat Commun. 2020 Nov 13;11(1):5759. doi: 10.1038/s41467-020-19611-1. PMID:33188213<ref>PMID:33188213</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 6yeg" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:08, 14 June 2023

OCA — Wed, 14 Jun 2023 11:08:15 GMT

←Older revision		Revision as of 11:08, 14 June 2023
Line 1:		Line 1:

	==Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - Final EM Refinement==		==Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - Final EM Refinement==
-	<StructureSection load='6yeg' size='340' side='right'caption='[[6yeg]], [[Resolution\|resolution]] 4.00Å~~, [[NMR_Ensembles_of_Models \| 1 NMR models]]~~' scene=''>	+	<StructureSection load='6yeg' size='340' side='right'caption='[[6yeg]], [[Resolution\|resolution]] 4.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6yeg]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bpspp Bpspp~~]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEG OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6YEG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yeg]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_phage_SPP1 Bacillus phage SPP1]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6YEG FirstGlance]. <br>
-	</td></tr>~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6yq5\|6yq5]]</div></td></tr>~~	+	</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=6yeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yeg OCA], [https://pdbe.org/6yeg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6yeg RCSB], [https://www.ebi.ac.uk/pdbsum/6yeg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6yeg ProSAT]</span></td></tr>
-	~~<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">17.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10724 BPSPP])</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=6yeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yeg OCA], [~~http~~://pdbe.org/6yeg PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6yeg RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6yeg PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6yeg ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/TUBE_BPSPP TUBE_BPSPP]] Forms the 160 nm long, sixfold helical, rigid tail tube. Binding to the entry receptor triggers structural rearrangements of the tail tube leading to ejection of the phage DNA into the host.<ref>PMID:17611601</ref> <ref>PMID:18786146</ref> <ref>PMID:25525268</ref> <ref>PMID:25991862</ref>	+	[https://www.uniprot.org/uniprot/TUBE_BPSPP TUBE_BPSPP] Forms the 160 nm long, sixfold helical, rigid tail tube. Binding to the entry receptor triggers structural rearrangements of the tail tube leading to ejection of the phage DNA into the host.<ref>PMID:17611601</ref> <ref>PMID:18786146</ref> <ref>PMID:25525268</ref> <ref>PMID:25991862</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacteriophage SPP1 is a double-stranded DNA virus of the Siphoviridae family that infects the bacterium Bacillus subtilis. This family of phages features a long, flexible, non-contractile tail that has been difficult to characterize structurally. Here, we present the atomic structure of the tail tube of phage SPP1. Our hybrid structure is based on the integration of structural restraints from solid-state nuclear magnetic resonance (NMR) and a density map from cryo-EM. We show that the tail tube protein gp17.1 organizes into hexameric rings that are stacked by flexible linker domains and, thus, form a hollow flexible tube with a negatively charged lumen suitable for the transport of DNA. Additionally, we assess the dynamics of the system by combining relaxation measurements with variances in density maps.
		+
		+	Architecture of the flexible tail tube of bacteriophage SPP1.,Zinke M, Sachowsky KAA, Oster C, Zinn-Justin S, Ravelli R, Schroder GF, Habeck M, Lange A Nat Commun. 2020 Nov 13;11(1):5759. doi: 10.1038/s41467-020-19611-1. PMID:33188213<ref>PMID:33188213</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6yeg" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bpspp~~]]	+	[[Category: Bacillus phage SPP1]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Habeck, M]]	+	[[Category: Habeck M]]
-	[[Category: Lange, A]]	+	[[Category: Lange A]]
-	[[Category: Ravelli, R]]	+	[[Category: Ravelli R]]
-	[[Category: Sachowsky~~, K A.A~~]]	+	[[Category: Sachowsky KAA]]
-	[[Category: Schroder~~, G F~~]]	+	[[Category: Schroder GF]]
-	[[Category: Zinke, M]]	+	[[Category: Zinke M]]
-	[[Category: Zinn-Justin, S]]	+	[[Category: Zinn-Justin S]]
-	~~[[Category: Complex]]~~	+
-	~~[[Category: Dna transport]]~~	+
-	~~[[Category: Scaffolding]]~~	+
-	~~[[Category: Tail tube]]~~	+
-	~~[[Category: Viral protein~~]]	+

OCA at 08:14, 2 December 2020

OCA — Wed, 02 Dec 2020 08:14:50 GMT

←Older revision		Revision as of 08:14, 2 December 2020
Line 1:		Line 1:

	==Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - Final EM Refinement==		==Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - Final EM Refinement==
-	<StructureSection load='6yeg' size='340' side='right'caption='[[6yeg]]' scene=''>	+	<StructureSection load='6yeg' size='340' side='right'caption='[[6yeg]], [[Resolution\|resolution]] 4.00Å, [[NMR_Ensembles_of_Models \| 1 NMR models]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full ~~crystallographic~~ information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YEG FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6yeg]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bpspp Bpspp]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YEG FirstGlance]. <br>
-	</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=6yeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yeg OCA], [http://pdbe.org/6yeg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yeg RCSB], [http://www.ebi.ac.uk/pdbsum/6yeg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yeg ProSAT]</span></td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[6yq5\|6yq5]]</div></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">17.1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=10724 BPSPP])</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=6yeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yeg OCA], [http://pdbe.org/6yeg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yeg RCSB], [http://www.ebi.ac.uk/pdbsum/6yeg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yeg ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TUBE_BPSPP TUBE_BPSPP]] Forms the 160 nm long, sixfold helical, rigid tail tube. Binding to the entry receptor triggers structural rearrangements of the tail tube leading to ejection of the phage DNA into the host.<ref>PMID:17611601</ref> <ref>PMID:18786146</ref> <ref>PMID:25525268</ref> <ref>PMID:25991862</ref>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bpspp]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Habeck M]]	+	[[Category: Habeck, M]]
-	[[Category: Lange A]]	+	[[Category: Lange, A]]
-	[[Category: Ravelli R]]	+	[[Category: Ravelli, R]]
-	[[Category: Sachowsky ~~KAA~~]]	+	[[Category: Sachowsky, K A.A]]
-	[[Category: Schroder GF]]	+	[[Category: Schroder, G F]]
-	[[Category: Zinke M]]	+	[[Category: Zinke, M]]
-	[[Category: Zinn-Justin S]]	+	[[Category: Zinn-Justin, S]]
		+	[[Category: Complex]]
		+	[[Category: Dna transport]]
		+	[[Category: Scaffolding]]
		+	[[Category: Tail tube]]
		+	[[Category: Viral protein]]

OCA at 05:49, 14 October 2020

OCA — Wed, 14 Oct 2020 05:49:44 GMT

←Older revision		Revision as of 05:49, 14 October 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6yeg is ON HOLD until Paper Publication~~	+	==Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM - Final EM Refinement==
-		+	<StructureSection load='6yeg' size='340' side='right'caption='[[6yeg]]' scene=''>
-	~~Authors: Zinke, M., Sachowsky, K.A.A., Zinn-Justin, S., Ravelli, R., Schroder, G.F., Habeck, M., Lange, A.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6YEG OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6YEG FirstGlance]. <br>
-	~~Description:~~ Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM -Final EM Refinement	+	</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=6yeg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6yeg OCA], [http://pdbe.org/6yeg PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6yeg RCSB], [http://www.ebi.ac.uk/pdbsum/6yeg PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6yeg ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Zinn~~-~~Justin~~, S]]	+	__TOC__
-	[[Category: Habeck, M]]	+	</StructureSection>
-	[[Category: Lange, A]]	+	[[Category: Large Structures]]
-	[[Category: ~~Zinke, M~~]]	+	[[Category: Habeck M]]
-	[[Category: Sachowsky~~, K.A.A~~]]	+	[[Category: Lange A]]
-	[[Category: ~~Ravelli, R~~]]	+	[[Category: Ravelli R]]
-	[[Category: ~~Schroder, G.F~~]]	+	[[Category: Sachowsky KAA]]
		+	[[Category: Schroder GF]]
		+	[[Category: Zinke M]]
		+	[[Category: Zinn-Justin S]]

OCA at 07:19, 22 July 2020

OCA — Wed, 22 Jul 2020 07:19:30 GMT

←Older revision		Revision as of 07:19, 22 July 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6yeg is ON HOLD	+	The entry 6yeg is ON HOLD until Paper Publication

	Authors: Zinke, M., Sachowsky, K.A.A., Zinn-Justin, S., Ravelli, R., Schroder, G.F., Habeck, M., Lange, A.		Authors: Zinke, M., Sachowsky, K.A.A., Zinn-Justin, S., Ravelli, R., Schroder, G.F., Habeck, M., Lange, A.

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

OCA — Wed, 01 Apr 2020 07:44:32 GMT

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

←Older revision

Revision as of 07:44, 1 April 2020

OCA: New page: '''Unreleased structure''' The entry 6yeg is ON HOLD Authors: Zinke, M., Sachowsky, K.A.A., Zinn-Justin, S., Ravelli, R., Schroder, G.F., Habeck, M., Lange, A. Description: Hybrid stru...

OCA — Wed, 01 Apr 2020 07:44:30 GMT

New page: '''Unreleased structure''' The entry 6yeg is ON HOLD Authors: Zinke, M., Sachowsky, K.A.A., Zinn-Justin, S., Ravelli, R., Schroder, G.F., Habeck, M., Lange, A. Description: Hybrid stru...

New page

'''Unreleased structure'''

The entry 6yeg is ON HOLD

Authors: Zinke, M., Sachowsky, K.A.A., Zinn-Justin, S., Ravelli, R., Schroder, G.F., Habeck, M., Lange, A.

Description: Hybrid structure of the SPP1 tail tube by solid-state NMR and cryo EM -Final EM Refinement
[[Category: Unreleased Structures]]
[[Category: Zinn-Justin, S]]
[[Category: Habeck, M]]
[[Category: Lange, A]]
[[Category: Zinke, M]]
[[Category: Sachowsky, K.A.A]]
[[Category: Ravelli, R]]
[[Category: Schroder, G.F]]