3rmx - Revision history

OCA at 12:30, 14 March 2024

OCA — Thu, 14 Mar 2024 12:30:04 GMT

←Older revision		Revision as of 12:30, 14 March 2024
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	<StructureSection load='3rmx' size='340' side='right'caption='[[3rmx]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='3rmx' size='340' side='right'caption='[[3rmx]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rmx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_botulinus"_van_ermengem_1896 "bacillus botulinus" van ermengem 1896~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RMX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rmx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Clostridium_botulinum Clostridium botulinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RMX 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;'>[[3n7j\|3n7j]], [[3rmy\|3rmy]]</div></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]] 2.75Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">botD, Botulinum Neurotoxin D ([https://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=1491 "Bacillus botulinus" van Ermengem 1896])~~</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=3rmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rmx OCA], [https://pdbe.org/3rmx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rmx RCSB], [https://www.ebi.ac.uk/pdbsum/3rmx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rmx 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=3rmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rmx OCA], [https://pdbe.org/3rmx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rmx RCSB], [https://www.ebi.ac.uk/pdbsum/3rmx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rmx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/~~BXD_CLOBO BXD_CLOBO]~~] Botulinum toxin ~~acts~~ by inhibiting neurotransmitter release. ~~It binds~~ to ~~peripheral neuronal synapses~~, ~~is internalized and moves~~ by ~~retrograde transport~~ up the ~~axon~~ into the ~~spinal cord where it can move between postsynaptic~~ and ~~presynaptic~~ neurons. It inhibits neurotransmitter release by acting as a zinc endopeptidase that cleaves the '60-Lys-\|-Leu-61' bond of ~~synaptobrevins~~-1 and -2.	+	[https://www.uniprot.org/uniprot/BXD_CBDP BXD_CBDP] Botulinum toxin causes flaccid paralysis by inhibiting neurotransmitter (acetylcholine) release from the presynaptic membranes of nerve terminals of the eukaryotic host skeletal and autonomic nervous system, with frequent heart or respiratory failure (PubMed:8175689, PubMed:16252491). Precursor of botulinum neurotoxin D for which a proteinaceous coreceptor is controversial. In double SV2A/SV2B knockout mice this toxin does not degrade its synaptobrevin target; introducing SV2A, SV2B or SV2C restores target cleavage (PubMed:21483489). Recognition of SV2 by this toxin does not occur via SV2 glycosylation or its large extracellular loop 4 (PubMed:21483489). Another group does not find a convincing interaction with SV2 (PubMed:21632541). Thus a protein receptor for this BoNT serotype has yet to be definitively proven. Recognizes at least 1 complex polysialylated ganglioside found on neural tissue. Electrical stimulation increases uptake of toxin in an ex vivo assay, presumably by transiently exposing a receptor usually found in eukaryotic target synaptic vesicles (PubMed:19650874, PubMed:21483489, PubMed:21632541). Upon synaptic vesicle recycling the toxin is taken up via the endocytic pathway; when the pH of the toxin-containing endosome drops a structural rearrangement occurs so that the N-terminus of the heavy chain (HC) forms pores that allows the light chain (LC) to translocate into the cytosol (By similarity). Once in the cytosol the disulfide bond linking the 2 subunits is reduced and LC cleaves its target protein on synaptic vesicles, preventing their fusion with the cytoplasmic membrane and thus neurotransmitter release (By similarity). Requires complex eukaryotic host polysialogangliosides for full neurotoxicity and for binding to neurons (PubMed:20704566, PubMed:21483489).[UniProtKB:P0DPI0]<ref>PMID:16252491</ref> <ref>PMID:19650874</ref> <ref>PMID:20704566</ref> <ref>PMID:21483489</ref> <ref>PMID:21632541</ref> <ref>PMID:8175689</ref> Has proteolytic activity (PubMed:8175689, PubMed:8197120). After translocation into the eukaryotic host cytosol, inhibits neurotransmitter release by acting as a zinc endopeptidase that cleaves the '61-Lys-\|-Leu-62' bond of synaptobrevin-1 (VAMP1), and the equivalent 'Lys-\|-Leu' sites in VAMP2 and VAMP3 (PubMed:8175689). Cleaves the '49-Lys-\|-Ile-50' bond of A.californica synaptobrevin (AC P35589) (PubMed:8197120). This chain probably has to be partially unfolded to translocate into the eukaryotic host cell cytosol (PubMed:15584922).<ref>PMID:8175689</ref> <ref>PMID:8197120</ref> <ref>PMID:15584922</ref> Responsible for host epithelial cell transcytosis, host nerve cell targeting and translocation of light chain (LC) into eukaryotic host cell cytosol. Composed of 3 subdomains; the translocation domain (TD), and N-terminus and C-terminus of the receptor-binding domain (RBD). The RBD is responsible for the adherence of the toxin to the eukaryotic target cell surface. The N-terminus of the TD wraps an extended belt around the perimeter of the LC, protecting Zn(2+) in the active site; it may also prevent premature LC dissociation from the translocation channel and protect toxin prior to translocation (PubMed:17907800). The TD inserts into synaptic vesicle membrane to allow translocation into the host cytosol (By similarity). The RBD binds eukaryotic host phosphatidylethanolamine, which may serve as toxin receptor (PubMed:16115873). Treatment of synaptosomes with proteinase K does not reduce HC binding, suggesting there is no protein receptor or it is protected from extracellular proteases (PubMed:16115873). HC significantly decreases uptake and toxicity of whole BoNT/D (PubMed:19650874, PubMed:21483489). HC also interferes with uptake of tetanus toxin (PubMed:19650874). Has 2 closely located carbohydrate-binding receptor sites and binds at least 1 GT1b ganglioside (PubMed:20704566). Bind gangliosides in the order GD2 > GT1b > GD1b (PubMed:21632541). Interacts with eukaryotic target protein SV2B (synaptic vesicle glycoprotein 2B) (PubMed:21483489). Expression of SV2A, SV2B or SV2C in mice knocked-out for the SV2 proteins restores entry of BoNT/D and cleavage of VAMP2, suggesting SV2 acts as its receptor (PubMed:21483489). Unlike BoNT/A and BoNT/E, toxin uptake is not mediated by large extracellular loop 4 of SV2 (PubMed:21483489). Another group finds very poor interaction with SV2 proteins, suggesting the possible protein receptor may not have been identified (PubMed:21632541).[UniProtKB:P0DPI0]<ref>PMID:16115873</ref> <ref>PMID:19650874</ref> <ref>PMID:20704566</ref> <ref>PMID:21483489</ref> <ref>PMID:21632541</ref> <ref>PMID:17907800</ref>
-	~~<div style="background~~-~~color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	~~Botulinum Neurotoxins~~ (~~BoNTs~~) ~~are organized into seven serotypes, A~~-G. ~~While several BoNT serotypes enter neurons through synaptic vesicle cycling utilizing dual receptors~~ (~~a ganglioside and a synaptic vesicle associated protein~~), the ~~entry pathway of BoNT/D is less well understood~~. ~~While BoNT~~/~~D entry is ganglioside dependent, alignment and structural studies show that BoNT~~/~~D lacks key residues within a conserved ganglioside binding pocket that are present in BoNT serotypes A, B, E, F~~, and ~~G, which indicate that BoNT/D-ganglioside interactions may be unique~~. ~~In this study, BoNT/D is shown to have a unique association with ganglioside relative to~~ the ~~other BoNT serotypes, utilizing a ganglioside binding loop~~ (~~GBL~~, ~~residues Tyr1235~~-~~Ala1245) within~~ the receptor binding domain ~~of BoNT/D~~ (~~HCR/D~~) ~~via b-series gangliosides, including GT1b, GD1b, and GD2~~. ~~HCR/D bound gangliosides and entered neurons dependent upon~~ the ~~aromatic ring~~ of ~~Phe1240 within~~ the ~~GBL. This is~~ the ~~first BoNT-ganglioside interaction that is mediated by a phenylalanine~~. ~~In contrast, Trp1238, located near the~~ N terminus of the ~~GBL~~, ~~was mostly solvent inaccessible~~ and ~~appeared~~ to ~~contribute~~ to ~~maintaining~~ the ~~loop structure~~. BoNT/D ~~entry and intoxication were enhanced by membrane depolarization via synaptic vesicle cycling~~, ~~where HCR/D colocalized~~ with ~~synaptophysin, a synaptic vesicle marker, but immunoprecipitation experiments did not detect direct association~~ with synaptic vesicle ~~protein 2~~ (~~SV2~~). ~~Thus~~, BoNT/D ~~utilizes unique associations with gangliosides~~ and ~~synaptic vesicles to enter neurons~~, ~~which may facilitate new neurotoxin therapies~~.	+
-		+
-	~~Novel ganglioside-~~mediated ~~entry~~ of ~~botulinum neurotoxin serotype D into neurons~~.,~~Kroken AR, Karalewitz AP, Fu Z, Kim JJ, Barbieri JT J Biol Chem. 2011 Jun 1~~. PMID:~~21632541~~<ref>PMID:~~21632541~~</ref>	+
-		+
-	~~From MEDLINE®~~/~~PubMed®, a database of the U.S. National Library of Medicine.~~<br>	+
-	</~~div~~>	+
-	<~~div class="pdbe-citations 3rmx" style="background-color~~:~~#fffaf0;"~~></~~div~~>	+

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus botulinus van ermengem 1896~~]]	+	[[Category: Clostridium botulinum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Barbieri~~, J T~~]]	+	[[Category: Barbieri JT]]
-	[[Category: Fu, Z]]	+	[[Category: Fu Z]]
-	[[Category: Karalewitz, A]]	+	[[Category: Karalewitz A]]
-	[[Category: Kim, J ~~J.P~~]]	+	[[Category: Kim J-JP]]
-	[[Category: Kroken, A]]	+	[[Category: Kroken A]]
-	~~[[Category: Botulinum neurotoxin]]~~	+
-	~~[[Category: F1240a]]~~	+
-	~~[[Category: Ganglioside binding loop]]~~	+
-	~~[[Category: Toxin~~]]	+

OCA at 10:17, 22 June 2022

OCA — Wed, 22 Jun 2022 10:17:42 GMT

←Older revision		Revision as of 10:17, 22 June 2022
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	==Crystal structure of HCR/D F1240A mutant==		==Crystal structure of HCR/D F1240A mutant==
-	<StructureSection load='3rmx' size='340' side='right' caption='[[3rmx]], [[Resolution\|resolution]] 2.75Å' scene=''>	+	<StructureSection load='3rmx' size='340' side='right'caption='[[3rmx]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rmx]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_botulinus"_van_ermengem_1896 "bacillus botulinus" van ermengem 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RMX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3RMX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rmx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_botulinus"_van_ermengem_1896 "bacillus botulinus" van ermengem 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3RMX FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n7j\|3n7j]], [[3rmy\|3rmy]]</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;'>[[3n7j\|3n7j]], [[3rmy\|3rmy]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">botD, Botulinum Neurotoxin D ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1491 "Bacillus botulinus" van Ermengem 1896])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">botD, Botulinum Neurotoxin D ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1491 "Bacillus botulinus" van Ermengem 1896])</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=3rmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rmx OCA], [~~http~~://pdbe.org/3rmx PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3rmx RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3rmx PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3rmx 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=3rmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rmx OCA], [https://pdbe.org/3rmx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3rmx RCSB], [https://www.ebi.ac.uk/pdbsum/3rmx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3rmx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/BXD_CLOBO BXD_CLOBO]] Botulinum toxin acts by inhibiting neurotransmitter release. It binds to peripheral neuronal synapses, is internalized and moves by retrograde transport up the axon into the spinal cord where it can move between postsynaptic and presynaptic neurons. It inhibits neurotransmitter release by acting as a zinc endopeptidase that cleaves the '60-Lys-\|-Leu-61' bond of synaptobrevins-1 and -2.	+	[[https://www.uniprot.org/uniprot/BXD_CLOBO BXD_CLOBO]] Botulinum toxin acts by inhibiting neurotransmitter release. It binds to peripheral neuronal synapses, is internalized and moves by retrograde transport up the axon into the spinal cord where it can move between postsynaptic and presynaptic neurons. It inhibits neurotransmitter release by acting as a zinc endopeptidase that cleaves the '60-Lys-\|-Leu-61' bond of synaptobrevins-1 and -2.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Botulinum neurotoxin\|Botulinum neurotoxin]]	+	*[[Botulinum neurotoxin 3D structures\|Botulinum neurotoxin 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacillus botulinus van ermengem 1896]]		[[Category: Bacillus botulinus van ermengem 1896]]
		+	[[Category: Large Structures]]
	[[Category: Barbieri, J T]]		[[Category: Barbieri, J T]]
	[[Category: Fu, Z]]		[[Category: Fu, Z]]

OCA at 11:13, 11 August 2016

OCA — Thu, 11 Aug 2016 11:13:42 GMT

←Older revision		Revision as of 11:13, 11 August 2016
Line 1:		Line 1:
		+
	==Crystal structure of HCR/D F1240A mutant==		==Crystal structure of HCR/D F1240A mutant==
	<StructureSection load='3rmx' size='340' side='right' caption='[[3rmx]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='3rmx' size='340' side='right' caption='[[3rmx]], [[Resolution\|resolution]] 2.75Å' scene=''>
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	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n7j\|3n7j]], [[3rmy\|3rmy]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n7j\|3n7j]], [[3rmy\|3rmy]]</td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">botD, Botulinum Neurotoxin D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1491 "Bacillus botulinus" van Ermengem 1896])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">botD, Botulinum Neurotoxin D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1491 "Bacillus botulinus" van Ermengem 1896])</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=3rmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rmx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rmx RCSB], [http://www.ebi.ac.uk/pdbsum/3rmx 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=3rmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rmx OCA], [http://pdbe.org/3rmx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3rmx RCSB], [http://www.ebi.ac.uk/pdbsum/3rmx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3rmx ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 17:		Line 18:
	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 3rmx" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Botulinum neurotoxin\|Botulinum neurotoxin]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:50, 7 February 2015

OCA — Sat, 07 Feb 2015 09:50:22 GMT

←Older revision		Revision as of 09:50, 7 February 2015
Line 2:		Line 2:
	<StructureSection load='3rmx' size='340' side='right' caption='[[3rmx]], [[Resolution\|resolution]] 2.75Å' scene=''>		<StructureSection load='3rmx' size='340' side='right' caption='[[3rmx]], [[Resolution\|resolution]] 2.75Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3rmx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Clostridium_botulinum Clostridium botulinum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RMX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3rmx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_botulinus"_van_ermengem_1896 "bacillus botulinus" van ermengem 1896]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RMX FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n7j\|3n7j]], [[3rmy\|3rmy]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n7j\|3n7j]], [[3rmy\|3rmy]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">botD, Botulinum Neurotoxin D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1491 ~~Clostridium botulinum~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">botD, Botulinum Neurotoxin D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1491 "Bacillus botulinus" van Ermengem 1896])</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=3rmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rmx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rmx RCSB], [http://www.ebi.ac.uk/pdbsum/3rmx 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=3rmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rmx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rmx RCSB], [http://www.ebi.ac.uk/pdbsum/3rmx PDBsum]</span></td></tr>
	</table>		</table>
Line 21:		Line 21:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Clostridium botulinum~~]]	+	[[Category: Bacillus botulinus van ermengem 1896]]
	[[Category: Barbieri, J T]]		[[Category: Barbieri, J T]]
	[[Category: Fu, Z]]		[[Category: Fu, Z]]
	[[Category: Karalewitz, A]]		[[Category: Karalewitz, A]]
-	[[Category: Kim, J-J P]]	+	[[Category: Kim, J J.P]]
	[[Category: Kroken, A]]		[[Category: Kroken, A]]
	[[Category: Botulinum neurotoxin]]		[[Category: Botulinum neurotoxin]]

OCA at 09:27, 25 December 2014

OCA — Thu, 25 Dec 2014 09:27:35 GMT

←Older revision		Revision as of 09:27, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3rmx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_botulinum Clostridium botulinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RMX FirstGlance]. <br>		<table><tr><td colspan='2'>[[3rmx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_botulinum Clostridium botulinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RMX FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n7j\|3n7j]], [[3rmy\|3rmy]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n7j\|3n7j]], [[3rmy\|3rmy]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">botD, Botulinum Neurotoxin D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1491 Clostridium botulinum])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">botD, Botulinum Neurotoxin D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1491 Clostridium botulinum])</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=3rmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rmx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rmx RCSB], [http://www.ebi.ac.uk/pdbsum/3rmx 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=3rmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rmx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rmx RCSB], [http://www.ebi.ac.uk/pdbsum/3rmx PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/BXD_CLOBO BXD_CLOBO]] Botulinum toxin acts by inhibiting neurotransmitter release. It binds to peripheral neuronal synapses, is internalized and moves by retrograde transport up the axon into the spinal cord where it can move between postsynaptic and presynaptic neurons. It inhibits neurotransmitter release by acting as a zinc endopeptidase that cleaves the '60-Lys-\|-Leu-61' bond of synaptobrevins-1 and -2.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 13:		Line 15:
	Novel ganglioside-mediated entry of botulinum neurotoxin serotype D into neurons.,Kroken AR, Karalewitz AP, Fu Z, Kim JJ, Barbieri JT J Biol Chem. 2011 Jun 1. PMID:21632541<ref>PMID:21632541</ref>		Novel ganglioside-mediated entry of botulinum neurotoxin serotype D into neurons.,Kroken AR, Karalewitz AP, Fu Z, Kim JJ, Barbieri JT J Biol Chem. 2011 Jun 1. PMID:21632541<ref>PMID:21632541</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, 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>
	== References ==		== References ==
Line 20:		Line 22:
	</StructureSection>		</StructureSection>
	[[Category: Clostridium botulinum]]		[[Category: Clostridium botulinum]]
-	[[Category: Barbieri, J T.]]	+	[[Category: Barbieri, J T]]
-	[[Category: Fu, Z.]]	+	[[Category: Fu, Z]]
-	[[Category: Karalewitz, A.]]	+	[[Category: Karalewitz, A]]
-	[[Category: Kim, J-J P.]]	+	[[Category: Kim, J-J P]]
-	[[Category: Kroken, A.]]	+	[[Category: Kroken, A]]
	[[Category: Botulinum neurotoxin]]		[[Category: Botulinum neurotoxin]]
	[[Category: F1240a]]		[[Category: F1240a]]
	[[Category: Ganglioside binding loop]]		[[Category: Ganglioside binding loop]]
	[[Category: Toxin]]		[[Category: Toxin]]

OCA at 04:44, 5 June 2014

OCA — Thu, 05 Jun 2014 04:44:37 GMT

←Older revision		Revision as of 04:44, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3rmx.~~png~~\|~~left~~\|~~200px~~]]	+	==Crystal structure of HCR/D F1240A mutant==
		+	<StructureSection load='3rmx' size='340' side='right' caption='[[3rmx]], [[Resolution\|resolution]] 2.75Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3rmx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_botulinum Clostridium botulinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3RMX FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[3n7j\|3n7j]], [[3rmy\|3rmy]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">botD, Botulinum Neurotoxin D ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1491 Clostridium botulinum])</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=3rmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3rmx OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3rmx RCSB], [http://www.ebi.ac.uk/pdbsum/3rmx PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Botulinum Neurotoxins (BoNTs) are organized into seven serotypes, A-G. While several BoNT serotypes enter neurons through synaptic vesicle cycling utilizing dual receptors (a ganglioside and a synaptic vesicle associated protein), the entry pathway of BoNT/D is less well understood. While BoNT/D entry is ganglioside dependent, alignment and structural studies show that BoNT/D lacks key residues within a conserved ganglioside binding pocket that are present in BoNT serotypes A, B, E, F, and G, which indicate that BoNT/D-ganglioside interactions may be unique. In this study, BoNT/D is shown to have a unique association with ganglioside relative to the other BoNT serotypes, utilizing a ganglioside binding loop (GBL, residues Tyr1235-Ala1245) within the receptor binding domain of BoNT/D (HCR/D) via b-series gangliosides, including GT1b, GD1b, and GD2. HCR/D bound gangliosides and entered neurons dependent upon the aromatic ring of Phe1240 within the GBL. This is the first BoNT-ganglioside interaction that is mediated by a phenylalanine. In contrast, Trp1238, located near the N terminus of the GBL, was mostly solvent inaccessible and appeared to contribute to maintaining the loop structure. BoNT/D entry and intoxication were enhanced by membrane depolarization via synaptic vesicle cycling, where HCR/D colocalized with synaptophysin, a synaptic vesicle marker, but immunoprecipitation experiments did not detect direct association with synaptic vesicle protein 2 (SV2). Thus, BoNT/D utilizes unique associations with gangliosides and synaptic vesicles to enter neurons, which may facilitate new neurotoxin therapies.

-	<!--	+	Novel ganglioside-mediated entry of botulinum neurotoxin serotype D into neurons.,Kroken AR, Karalewitz AP, Fu Z, Kim JJ, Barbieri JT J Biol Chem. 2011 Jun 1. PMID:21632541<ref>PMID:21632541</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3rmx"~~, ~~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_3rmx\| PDB=3rmx \| SCENE= }}~~	+

-	~~===Crystal structure of HCR~~/~~D F1240A mutant===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_21632541}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 21632541 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_21632541}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3rmx]] is a 4 chain structure with sequence from [http:~~/~~/en.wikipedia.org/wiki/Clostridium_botulinum Clostridium botulinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RMX OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:021632541<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Clostridium botulinum]]		[[Category: Clostridium botulinum]]
	[[Category: Barbieri, J T.]]		[[Category: Barbieri, J T.]]

OCA at 04:55, 10 August 2011

OCA — Wed, 10 Aug 2011 04:55:18 GMT

←Older revision		Revision as of 04:55, 10 August 2011
Line 1:		Line 1:
-	[[Image:3rmx.~~jpg~~\|left\|200px]]	+	[[Image:3rmx.png\|left\|200px]]

	<!--		<!--

OCA at 15:48, 22 June 2011

OCA — Wed, 22 Jun 2011 15:48:42 GMT

←Older revision		Revision as of 15:48, 22 June 2011
Line 11:		Line 11:
	===Crystal structure of HCR/D F1240A mutant===		===Crystal structure of HCR/D F1240A mutant===

		+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_21632541}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 21632541 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_21632541}}

	==About this Structure==		==About this Structure==
	[[3rmx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_botulinum Clostridium botulinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RMX OCA].		[[3rmx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_botulinum Clostridium botulinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RMX OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:021632541</ref><references group="xtra"/>
	[[Category: Clostridium botulinum]]		[[Category: Clostridium botulinum]]
	[[Category: Barbieri, J T.]]		[[Category: Barbieri, J T.]]
Line 20:		Line 29:
	[[Category: Kim, J-J P.]]		[[Category: Kim, J-J P.]]
	[[Category: Kroken, A.]]		[[Category: Kroken, A.]]
		+	[[Category: Botulinum neurotoxin]]
		+	[[Category: F1240a]]
		+	[[Category: Ganglioside binding loop]]
		+	[[Category: Toxin]]

OCA at 06:00, 1 June 2011

OCA — Wed, 01 Jun 2011 06:00:34 GMT

←Older revision		Revision as of 06:00, 1 June 2011
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3rmx.jpg\|left\|200px]]

-	The ~~entry 3rmx~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3rmx", 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_3rmx\| PDB=3rmx \| SCENE= }}

-	~~Authors: Fu, Z., Karalewitz, A., Kroken, A., Kim, J-J.P., Barbieri, J.T.~~	+	===Crystal structure of HCR/D F1240A mutant===

-	~~Description: Crystal~~ structure ~~of HCR~~/~~D F1240A mutant~~	+
		+	==About this Structure==
		+	[[3rmx]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Clostridium_botulinum Clostridium botulinum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3RMX OCA].
		+	[[Category: Clostridium botulinum]]
		+	[[Category: Barbieri, J T.]]
		+	[[Category: Fu, Z.]]
		+	[[Category: Karalewitz, A.]]
		+	[[Category: Kim, J-J P.]]
		+	[[Category: Kroken, A.]]

OCA at 05:13, 18 May 2011

OCA — Wed, 18 May 2011 05:13:43 GMT

←Older revision		Revision as of 05:13, 18 May 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3rmx is ON HOLD	+	The entry 3rmx is ON HOLD until Paper Publication

	Authors: Fu, Z., Karalewitz, A., Kroken, A., Kim, J-J.P., Barbieri, J.T.		Authors: Fu, Z., Karalewitz, A., Kroken, A., Kim, J-J.P., Barbieri, J.T.

	Description: Crystal structure of HCR/D F1240A mutant		Description: Crystal structure of HCR/D F1240A mutant