4rdr: Difference between revisions

Revision as of 06:50, 2 March 2023

Structure of the bacterial Zn-transporter ZnuD from Neisseria meningitidis (locked conformation bound to zinc and cadmium ions)

Structural highlights

4rdr is a 1 chain structure with sequence from Neisseria meningitidis MC58. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	C8E, CD, EDO, GOL, MSE, SO4, ZN
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

Y964_NEIMB Probable receptor, TonB-dependent.

Publication Abstract from PubMed

Invading bacteria from the Neisseriaceae, Acinetobacteriaceae, Bordetellaceae and Moraxellaceae families express the conserved outer-membrane zinc transporter zinc-uptake component D (ZnuD) to overcome nutritional restriction imposed by the host organism during infection. Here we demonstrate that ZnuD is required for efficient systemic infections by the causative agent of bacterial meningitis, Neisseria meningitidis, in a mouse model. We also combine X-ray crystallography and molecular dynamics simulations to gain insight into the mechanism of zinc recognition and transport across the bacterial outer-membrane by ZnuD. Because ZnuD is also considered a promising vaccine candidate against N. meningitidis, we use several ZnuD structural intermediates to map potential antigenic epitopes, and propose a mechanism by which ZnuD can maintain high sequence conservation yet avoid immune recognition by altering the conformation of surface-exposed loops.

The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD.,Calmettes C, Ing C, Buckwalter CM, El Bakkouri M, Chieh-Lin Lai C, Pogoutse A, Gray-Owen SD, Pomes R, Moraes TF Nat Commun. 2015 Aug 18;6:7996. doi: 10.1038/ncomms8996. PMID:26282243^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Calmettes C, Ing C, Buckwalter CM, El Bakkouri M, Chieh-Lin Lai C, Pogoutse A, Gray-Owen SD, Pomes R, Moraes TF. The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD. Nat Commun. 2015 Aug 18;6:7996. doi: 10.1038/ncomms8996. PMID:26282243 doi:https://dx.doi.org/10.1038/ncomms8996

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OCA

[1] Calmettes C, Ing C, Buckwalter CM, El Bakkouri M, Chieh-Lin Lai C, Pogoutse A, Gray-Owen SD, Pomes R, Moraes TF. The molecular mechanism of Zinc acquisition by the neisserial outer-membrane transporter ZnuD. Nat Commun. 2015 Aug 18;6:7996. doi: 10.1038/ncomms8996. PMID:26282243 doi:https://dx.doi.org/10.1038/ncomms8996

[1]

@@ Line 1: / Line 1: @@
 ==Structure of the bacterial Zn-transporter ZnuD from Neisseria meningitidis (locked conformation bound to zinc and cadmium ions)==
-<StructureSection load='4rdr' size='340' side='right' caption='[[4rdr]], [[Resolution|resolution]] 2.47&Aring;' scene=''>
+<StructureSection load='4rdr' size='340' side='right'caption='[[4rdr]], [[Resolution|resolution]] 2.47&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4rdr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Neimb Neimb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RDR OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4RDR FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4rdr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Neisseria_meningitidis_MC58 Neisseria meningitidis MC58]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4RDR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4RDR FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4rdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rdr OCA], [https://pdbe.org/4rdr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4rdr RCSB], [https://www.ebi.ac.uk/pdbsum/4rdr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4rdr ProSAT]</span></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4rdt|4rdt]]</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NMB0964 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=122586 NEIMB])</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=4rdr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4rdr OCA], [http://pdbe.org/4rdr PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4rdr RCSB], [http://www.ebi.ac.uk/pdbsum/4rdr PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4rdr ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/Y964_NEIMB Y964_NEIMB]] Probable receptor, TonB-dependent.
+[https://www.uniprot.org/uniprot/Y964_NEIMB Y964_NEIMB] Probable receptor, TonB-dependent.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 22: @@
 __TOC__
 </StructureSection>
-[[Category: Neimb]]
+[[Category: Large Structures]]
-[[Category: Calmettes, C]]
+[[Category: Neisseria meningitidis MC58]]
-[[Category: Moraes, T F]]
+[[Category: Calmettes C]]
-[[Category: Membrane protein]]
+[[Category: Moraes TF]]
-[[Category: Outer membrane protein]]
-[[Category: Tonb dependent receptor]]
-[[Category: Vaccine candidate]]
-[[Category: Zinc acquisition]]
-[[Category: Zinc transporter]]

4rdr: Difference between revisions

Revision as of 06:50, 2 March 2023

Structure of the bacterial Zn-transporter ZnuD from Neisseria meningitidis (locked conformation bound to zinc and cadmium ions)

Structural highlights

Function

Publication Abstract from PubMed

References

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