3n7j

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==Crystal structure of botulinum neurotoxin serotype D binding domain==
==Crystal structure of botulinum neurotoxin serotype D binding domain==
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<StructureSection load='3n7j' size='340' side='right' caption='[[3n7j]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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<StructureSection load='3n7j' size='340' side='right'caption='[[3n7j]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3n7j]] is a 1 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=3N7J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3N7J FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3n7j]] is a 1 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=3N7J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N7J FirstGlance]. <br>
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</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3n7k|3n7k]], [[3n7l|3n7l]], [[3n7m|3n7m]]</td></tr>
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</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&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">botD, Clostridium phage d-16 phi ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1491 "Bacillus botulinus" van Ermengem 1896])</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3n7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n7j OCA], [https://pdbe.org/3n7j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n7j RCSB], [https://www.ebi.ac.uk/pdbsum/3n7j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n7j ProSAT]</span></td></tr>
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<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=3n7j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n7j OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3n7j RCSB], [http://www.ebi.ac.uk/pdbsum/3n7j PDBsum]</span></td></tr>
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</table>
</table>
== Function ==
== Function ==
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[[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.
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[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>
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
<jmolCheckbox>
<jmolCheckbox>
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<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n7/3n7j_consurf.spt"</scriptWhenChecked>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/n7/3n7j_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>
</jmolCheckbox>
</jmolCheckbox>
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</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].
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</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=3n7j ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
</div>
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<div class="pdbe-citations 3n7j" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Botulinum neurotoxin 3D structures|Botulinum neurotoxin 3D structures]]
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Bacillus botulinus van ermengem 1896]]
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[[Category: Clostridium botulinum]]
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[[Category: Baldwin, M R]]
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[[Category: Large Structures]]
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[[Category: Barbieri, J T]]
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[[Category: Baldwin MR]]
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[[Category: Fu, Z]]
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[[Category: Barbieri JT]]
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[[Category: Karalewitz, A]]
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[[Category: Fu Z]]
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[[Category: Kim, J J.P]]
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[[Category: Karalewitz A]]
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[[Category: Kroken, A]]
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[[Category: Kim J-JP]]
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[[Category: Botulinum neurotoxin]]
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[[Category: Kroken A]]
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[[Category: Ganglioside binding loop]]
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[[Category: Hcr/d]]
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[[Category: Toxin]]
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Current revision

Crystal structure of botulinum neurotoxin serotype D binding domain

PDB ID 3n7j

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