6jzk - Revision history

OCA at 10:22, 22 November 2023

OCA — Wed, 22 Nov 2023 10:22:26 GMT

←Older revision		Revision as of 10:22, 22 November 2023
Line 3:		Line 3:
	<StructureSection load='6jzk' size='340' side='right'caption='[[6jzk]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='6jzk' size='340' side='right'caption='[[6jzk]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jzk]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Porg3 Porg3~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JZK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6JZK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jzk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Porphyromonas_gingivalis_ATCC_33277 Porphyromonas gingivalis ATCC 33277]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JZK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JZK FirstGlance]. <br>
-	</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>~~, ~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SRT:S,R+MESO-TARTARIC+ACID'>SRT</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]] 2.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[6jzj\|6jzj]]~~<~~/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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SRT:S,R+MESO-TARTARIC+ACID'>SRT</scene></td></tr>
-	<~~tr id~~='~~gene~~'><~~td class="sblockLbl"~~><~~b>[[Gene\|Gene~~:~~]]</b~~></td>~~<td class="sblockDat">fimA, PGN_0180 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=431947 PORG3])~~</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=6jzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jzk OCA], [https://pdbe.org/6jzk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jzk RCSB], [https://www.ebi.ac.uk/pdbsum/6jzk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jzk 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=6jzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jzk OCA], [~~http~~://pdbe.org/6jzk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jzk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jzk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jzk ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/FIMA1_PORG3 FIMA1_PORG3]] Structural subunit of the major fimbriae. These long, filamentous pili are attached to the cell surface; they mediate biofilm formation, adhesion onto host cells and onto other bacteria that are part of the oral microbiome (PubMed:9786913, PubMed:12593606, PubMed:15165251, PubMed:17675496, PubMed:17526848, PubMed:20530728, PubMed:27062925). They play an important role in the invasion of periodontal tissues (PubMed:12593606). Fimbriae and their constituents are major virulence factors. FimA proteins from different strains have highly divergent sequences, and this has been used for classification (PubMed:23809984). The sequence-based classification correlates with pathogenicity (PubMed:17675496).<ref>PMID:12593606</ref> <ref>PMID:15165251</ref> <ref>PMID:17526848</ref> <ref>PMID:17675496</ref> <ref>PMID:20530728</ref> <ref>PMID:23809984</ref> <ref>PMID:27062925</ref> <ref>PMID:9786913</ref>	+	[https://www.uniprot.org/uniprot/FIMA1_PORG3 FIMA1_PORG3] Structural subunit of the major fimbriae. These long, filamentous pili are attached to the cell surface; they mediate biofilm formation, adhesion onto host cells and onto other bacteria that are part of the oral microbiome (PubMed:9786913, PubMed:12593606, PubMed:15165251, PubMed:17675496, PubMed:17526848, PubMed:20530728, PubMed:27062925). They play an important role in the invasion of periodontal tissues (PubMed:12593606). Fimbriae and their constituents are major virulence factors. FimA proteins from different strains have highly divergent sequences, and this has been used for classification (PubMed:23809984). The sequence-based classification correlates with pathogenicity (PubMed:17675496).<ref>PMID:12593606</ref> <ref>PMID:15165251</ref> <ref>PMID:17526848</ref> <ref>PMID:17675496</ref> <ref>PMID:20530728</ref> <ref>PMID:23809984</ref> <ref>PMID:27062925</ref> <ref>PMID:9786913</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Porg3~~]]	+	[[Category: Porphyromonas gingivalis ATCC 33277]]
-	[[Category: Imada, K]]	+	[[Category: Imada K]]
-	[[Category: Nakayam, K]]	+	[[Category: Nakayam K]]
-	[[Category: Okada, K]]	+	[[Category: Okada K]]
-	[[Category: Shoji, M]]	+	[[Category: Shoji M]]
-	~~[[Category: Cell adhesion]]~~	+
-	~~[[Category: Major fimbrial subunit protein]]~~	+
-	~~[[Category: Type v pili~~]]	+

OCA at 06:57, 29 April 2020

OCA — Wed, 29 Apr 2020 06:57:56 GMT

←Older revision		Revision as of 06:57, 29 April 2020
Line 1:		Line 1:

	==Structure of FimA type-1 (FimA1) prepilin of the type V major fimbrium==		==Structure of FimA type-1 (FimA1) prepilin of the type V major fimbrium==
-	<StructureSection load='6jzk' size='340' side='right'caption='[[6jzk]]' scene=''>	+	<StructureSection load='6jzk' size='340' side='right'caption='[[6jzk]], [[Resolution\|resolution]] 2.10Å' 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=6JZK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JZK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jzk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Porg3 Porg3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JZK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JZK 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=6jzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jzk OCA], [http://pdbe.org/6jzk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jzk RCSB], [http://www.ebi.ac.uk/pdbsum/6jzk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jzk ProSAT]</span></td></tr>	+	</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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=SRT:S,R+MESO-TARTARIC+ACID'>SRT</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[6jzj\|6jzj]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">fimA, PGN_0180 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=431947 PORG3])</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=6jzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jzk OCA], [http://pdbe.org/6jzk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jzk RCSB], [http://www.ebi.ac.uk/pdbsum/6jzk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jzk ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/FIMA1_PORG3 FIMA1_PORG3]] Structural subunit of the major fimbriae. These long, filamentous pili are attached to the cell surface; they mediate biofilm formation, adhesion onto host cells and onto other bacteria that are part of the oral microbiome (PubMed:9786913, PubMed:12593606, PubMed:15165251, PubMed:17675496, PubMed:17526848, PubMed:20530728, PubMed:27062925). They play an important role in the invasion of periodontal tissues (PubMed:12593606). Fimbriae and their constituents are major virulence factors. FimA proteins from different strains have highly divergent sequences, and this has been used for classification (PubMed:23809984). The sequence-based classification correlates with pathogenicity (PubMed:17675496).<ref>PMID:12593606</ref> <ref>PMID:15165251</ref> <ref>PMID:17526848</ref> <ref>PMID:17675496</ref> <ref>PMID:20530728</ref> <ref>PMID:23809984</ref> <ref>PMID:27062925</ref> <ref>PMID:9786913</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Bacterial adhesion is a general strategy for host-microbe and microbe-microbe interactions. Adhesive pili are essential for colonization, biofilm formation, virulence and pathogenesis of many environmental and pathogenic bacteria(1,2). Members of the class Bacteroidia have unique type V pili, assembled by protease-mediated polymerization(3). Porphyromonas gingivalis is the main contributor to periodontal disease and its type V pili are a key factor for its virulence(4). However, the structure of the polymerized pilus and its assembly mechanism are unknown. Here we show structures of polymerized and monomeric states of FimA stalk pilin from P. gingivalis, determined by cryo-electron microscopy and crystallography. The atomic model of assembled FimA shows that the C-terminal strand of a donor subunit is inserted into a groove in the beta-sheet of an acceptor subunit after N-terminal cleavage by the protease RgpB. The C terminus of the donor strand is essential for polymerization. We propose that type V pili assemble via a sequential polar assembly mechanism at the cell surface, involving protease-mediated strand exchange, employed by various Gram-negative species belonging to the class Bacteroidia. Our results reveal functional surfaces related to pathogenic properties of polymerized FimA. These insights may facilitate development of antibacterial drugs.
		+
		+	Structure of polymerized type V pilin reveals assembly mechanism involving protease-mediated strand exchange.,Shibata S, Shoji M, Okada K, Matsunami H, Matthews MM, Imada K, Nakayama K, Wolf M Nat Microbiol. 2020 Apr 13. pii: 10.1038/s41564-020-0705-1. doi:, 10.1038/s41564-020-0705-1. PMID:32284566<ref>PMID:32284566</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6jzk" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Imada K]]	+	[[Category: Porg3]]
-	[[Category: Nakayam K]]	+	[[Category: Imada, K]]
-	[[Category: Okada K]]	+	[[Category: Nakayam, K]]
-	[[Category: Shoji M]]	+	[[Category: Okada, K]]
		+	[[Category: Shoji, M]]
		+	[[Category: Cell adhesion]]
		+	[[Category: Major fimbrial subunit protein]]
		+	[[Category: Type v pili]]

OCA at 06:51, 15 April 2020

OCA — Wed, 15 Apr 2020 06:51:26 GMT

←Older revision		Revision as of 06:51, 15 April 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry 6jzk is ON HOLD until Paper Publication~~	+	==Structure of FimA type-1 (FimA1) prepilin of the type V major fimbrium==
-		+	<StructureSection load='6jzk' size='340' side='right'caption='[[6jzk]]' scene=''>
-	~~Authors: Okada, K., Shoji, M., Nakayam, K., Imada, K.~~	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JZK OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6JZK FirstGlance]. <br>
-	~~Description:~~ Structure of FimA type-1 (FimA1) prepilin of the type V major fimbrium	+	</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=6jzk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jzk OCA], [http://pdbe.org/6jzk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jzk RCSB], [http://www.ebi.ac.uk/pdbsum/6jzk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jzk ProSAT]</span></td></tr>
-	[[~~Category~~: ~~Unreleased Structures~~]]	+	</table>
-	[[~~Category~~: ~~Okada~~, K]]	+	__TOC__
-	[[Category: ~~Shoji, M~~]]	+	</StructureSection>
-	[[Category: Imada, K]]	+	[[Category: Large Structures]]
-	[[Category: Nakayam, K]]	+	[[Category: Imada K]]
		+	[[Category: Nakayam K]]
		+	[[Category: Okada K]]
		+	[[Category: Shoji M]]

OCA at 06:29, 2 October 2019

OCA — Wed, 02 Oct 2019 06:29:05 GMT

←Older revision		Revision as of 06:29, 2 October 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

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

	Authors: Okada, K., Shoji, M., Nakayam, K., Imada, K.		Authors: Okada, K., Shoji, M., Nakayam, K., Imada, K.

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

OCA — Fri, 10 May 2019 07:41:09 GMT

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

←Older revision

Revision as of 07:41, 10 May 2019

OCA: New page: '''Unreleased structure''' The entry 6jzk is ON HOLD Authors: Okada, K., Shoji, M., Nakayam, K., Imada, K. Description: Structure of FimA type-1 (FimA1) prepilin of the type V major fi...

OCA — Fri, 10 May 2019 07:41:05 GMT

New page: '''Unreleased structure''' The entry 6jzk is ON HOLD Authors: Okada, K., Shoji, M., Nakayam, K., Imada, K. Description: Structure of FimA type-1 (FimA1) prepilin of the type V major fi...

New page

'''Unreleased structure'''

The entry 6jzk is ON HOLD

Authors: Okada, K., Shoji, M., Nakayam, K., Imada, K.

Description: Structure of FimA type-1 (FimA1) prepilin of the type V major fimbrium
[[Category: Unreleased Structures]]
[[Category: Okada, K]]
[[Category: Shoji, M]]
[[Category: Imada, K]]
[[Category: Nakayam, K]]