This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3hwb

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 11:59, 30 March 2022

Cation selective pathway of OmpF porin revealed by anomalous diffraction

Structural highlights

3hwb is a 2 chain structure with sequence from Ecoli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Related:	3hw9
Gene:	ompF, cmlB, coa, cry, tolF, b0929, JW0912 (ECOLI)
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]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The OmpF porin from the Escherichia coli outer membrane folds into a trimer of beta-barrels, each forming a wide aqueous pore allowing the passage of ions and small solutes. A long loop (L3) carrying multiple acidic residues folds into the beta-barrel pore to form a narrow "constriction zone". A strong and highly conserved charge asymmetry is observed at the constriction zone, with multiple basic residues attached to the wall of the beta-barrel (Lys16, Arg42, Arg82 and Arg132) on one side, and multiple acidic residues of L3 (Asp107, Asp113, Glu117, Asp121, Asp126, Asp127) on the other side. Several computational studies have suggested that a strong transverse electric field could exist at the constriction zone as a result of such charge asymmetry, giving rise to separate permeation pathways for cations and anions. To examine this question, OmpF was expressed, purified and crystallized in the P6(3) space group and two different data sets were obtained at 2.6 A and 3.0 A resolution with K(+) and Rb(+), respectively. The Rb(+)-soaked crystals were collected at the rubidium anomalous wavelength of 0.8149 A and cation positions were determined. A PEG molecule was observed in the pore region for both the K(+) and Rb(+)-soaked crystals, where it interacts with loop L3. The results reveal the separate pathways of anions and cations across the constriction zone of the OmpF pore.

Cation-selective pathway of OmpF porin revealed by anomalous X-ray diffraction.,Dhakshnamoorthy B, Raychaudhury S, Blachowicz L, Roux B J Mol Biol. 2010 Feb 19;396(2):293-300. Epub 2009 Nov 20. PMID:19932117^[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, Raychaudhury S, Blachowicz L, Roux B. Cation-selective pathway of OmpF porin revealed by anomalous X-ray diffraction. J Mol Biol. 2010 Feb 19;396(2):293-300. Epub 2009 Nov 20. PMID:19932117 doi:10.1016/j.jmb.2009.11.042

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3hwb"

@@ Line 1: / Line 1: @@
 ==Cation selective pathway of OmpF porin revealed by anomalous diffraction==
-<StructureSection load='3hwb' size='340' side='right' caption='[[3hwb]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+<StructureSection load='3hwb' size='340' side='right'caption='[[3hwb]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3hwb]] is a 2 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=3HWB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3HWB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3hwb]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Ecoli Ecoli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3HWB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3HWB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=RB:RUBIDIUM+ION'>RB</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3hw9|3hw9]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3hw9|3hw9]]</div></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ompF, cmlB, coa, cry, tolF, b0929, JW0912 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83333 ECOLI])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ompF, cmlB, coa, cry, tolF, b0929, JW0912 ([https://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3hwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwb OCA], [http://pdbe.org/3hwb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3hwb RCSB], [http://www.ebi.ac.uk/pdbsum/3hwb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3hwb 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=3hwb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3hwb OCA], [https://pdbe.org/3hwb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3hwb RCSB], [https://www.ebi.ac.uk/pdbsum/3hwb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3hwb 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>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 32: / Line 32: @@
 ==See Also==
-*[[Porin|Porin]]
+*[[Porin 3D structures|Porin 3D structures]]
 == References ==
 <references/>
@@ Line 38: / Line 38: @@
 </StructureSection>
 [[Category: Ecoli]]
+[[Category: Large Structures]]
 [[Category: Balasundaresan, D]]
 [[Category: Blachowicz, L]]

3hwb

From Proteopedia

Revision as of 11:59, 30 March 2022

Cation selective pathway of OmpF porin revealed by anomalous diffraction

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox