4lse: Difference between revisions

Latest revision as of 16:24, 20 September 2023

Ion selectivity of OmpF porin soaked in 0.2M NaBr

Structural highlights

4lse is a 3 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	BR, C8E, MG, PEG
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

OMPF_ECOLI Forms pores that allow passive diffusion of small molecules across the outer membrane. It is also a receptor for the bacteriophage T2.^[1]

Publication Abstract from PubMed

OmpF, a multiionic porin from Escherichia coli, is a useful protypical model system for addressing general questions about electrostatic interactions in the confinement of an aqueous molecular pore. Here, anion binding sites in the OmpF pore were mapped by anomalous X-ray scattering of Br- ions from four different crystal structures and compared with Mg2+ sites and Rb+ sites from a previous anomalous diffraction study to provide a complete picture of cation and anion transfer paths along the OmpF channel. By comparing structures with various crystallization conditions, we find that anions bind in discrete clusters along the entire length of the OmpF pore, whereas cations find conserved binding sites with the extracellular, surface-exposed loops. Results from molecular dynamics simulations are consistent with the experimental data and help highlight the critical residues that preferentially contact either cations or anions during permeation. Analysis of these results provides new insights into the molecular mechanisms that determine ion selectivity in OmpF porin.

A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations.,Dhakshnamoorthy B, Ziervogel BK, Blachowicz L, Roux B J Am Chem Soc. 2013 Oct 9. PMID:24106986^[2]

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

References

↑ Duval V, Nicoloff H, Levy SB. Combined inactivation of lon and ycgE decreases multidrug susceptibility by reducing the amount of OmpF porin in Escherichia coli. Antimicrob Agents Chemother. 2009 Nov;53(11):4944-8. doi: 10.1128/AAC.00787-09., Epub 2009 Aug 31. PMID:19721064 doi:10.1128/AAC.00787-09
↑ Dhakshnamoorthy B, Ziervogel BK, Blachowicz L, Roux B. A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations. J Am Chem Soc. 2013 Oct 9. PMID:24106986 doi:https://dx.doi.org/10.1021/ja407783a

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OCA

[1] Duval V, Nicoloff H, Levy SB. Combined inactivation of lon and ycgE decreases multidrug susceptibility by reducing the amount of OmpF porin in Escherichia coli. Antimicrob Agents Chemother. 2009 Nov;53(11):4944-8. doi: 10.1128/AAC.00787-09., Epub 2009 Aug 31. PMID:19721064 doi:10.1128/AAC.00787-09

[2] Dhakshnamoorthy B, Ziervogel BK, Blachowicz L, Roux B. A structural study of ion permeation in OmpF porin from anomalous X-ray diffraction and molecular dynamics simulations. J Am Chem Soc. 2013 Oct 9. PMID:24106986 doi:https://dx.doi.org/10.1021/ja407783a

[1]

[2]

@@ Line 1: / Line 1: @@
 ==Ion selectivity of OmpF porin soaked in 0.2M NaBr==
-<StructureSection load='4lse' size='340' side='right' caption='[[4lse]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
+<StructureSection load='4lse' size='340' side='right'caption='[[4lse]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[4lse]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LSE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4LSE FirstGlance]. <br>
+<table><tr><td colspan='2'>[[4lse]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4LSE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4LSE FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.1&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4lsf|4lsf]], [[4lsh|4lsh]], [[4lsi|4lsi]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=C8E:(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE'>C8E</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">b0929, cmlB, coa, cry, JW0912, ompF, tolF ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</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=4lse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lse OCA], [https://pdbe.org/4lse PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4lse RCSB], [https://www.ebi.ac.uk/pdbsum/4lse PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4lse ProSAT]</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=4lse FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4lse OCA], [http://pdbe.org/4lse PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4lse RCSB], [http://www.ebi.ac.uk/pdbsum/4lse PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4lse ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/OMPF_ECOLI OMPF_ECOLI]] Forms pores that allow passive diffusion of small molecules across the outer membrane. It is also a receptor for the bacteriophage T2.<ref>PMID:19721064</ref>
+[https://www.uniprot.org/uniprot/OMPF_ECOLI OMPF_ECOLI] Forms pores that allow passive diffusion of small molecules across the outer membrane. It is also a receptor for the bacteriophage T2.<ref>PMID:19721064</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 22: / Line 21: @@
 ==See Also==
-*[[Porin|Porin]]
+*[[Porin 3D structures|Porin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Ecoli]]
+[[Category: Escherichia coli K-12]]
-[[Category: Balasundaresan, D]]
+[[Category: Large Structures]]
-[[Category: Blachowicz, L]]
+[[Category: Balasundaresan D]]
-[[Category: Roux, B]]
+[[Category: Blachowicz L]]
-[[Category: Beta-barrel]]
+[[Category: Roux B]]
-[[Category: Ion transport]]
-[[Category: Outer membrane protein]]
-[[Category: Porin]]
-[[Category: Transport protein]]

4lse: Difference between revisions

Latest revision as of 16:24, 20 September 2023

Ion selectivity of OmpF porin soaked in 0.2M NaBr

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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