|
|
| (3 intermediate revisions not shown.) |
| Line 4: |
Line 4: |
| | == Structural highlights == | | == Structural highlights == |
| | <table><tr><td colspan='2'>[[2y5m]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevibacillus_brevis Brevibacillus brevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y5M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y5M FirstGlance]. <br> | | <table><tr><td colspan='2'>[[2y5m]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Brevibacillus_brevis Brevibacillus brevis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Y5M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Y5M FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=15P:POLYETHYLENE+GLYCOL+(N=34)'>15P</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]] 1.08Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=DLE:D-LEUCINE'>DLE</scene>, <scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=FVA:N-FORMYL-L-VALINE'>FVA</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=15P:POLYETHYLENE+GLYCOL+(N=34)'>15P</scene>, <scene name='pdbligand=DLE:D-LEUCINE'>DLE</scene>, <scene name='pdbligand=DVA:D-VALINE'>DVA</scene>, <scene name='pdbligand=ETA:ETHANOLAMINE'>ETA</scene>, <scene name='pdbligand=FVA:N-FORMYL-L-VALINE'>FVA</scene>, <scene name='pdbligand=PRD_000150:GRAMICIDIN+A'>PRD_000150</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1nt6|1nt6]], [[1jo3|1jo3]], [[1alz|1alz]], [[1grm|1grm]], [[1jo4|1jo4]], [[1bdw|1bdw]], [[1nru|1nru]], [[1w5u|1w5u]], [[1tkq|1tkq]], [[1mag|1mag]], [[2izq|2izq]], [[1c4d|1c4d]], [[1av2|1av2]], [[1kqe|1kqe]], [[1mic|1mic]], [[1nt5|1nt5]], [[1al4|1al4]], [[1gmk|1gmk]], [[1ng8|1ng8]], [[1nrm|1nrm]], [[1jno|1jno]], [[1alx|1alx]], [[2xdc|2xdc]], [[2y6n|2y6n]]</div></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=2y5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y5m OCA], [https://pdbe.org/2y5m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y5m RCSB], [https://www.ebi.ac.uk/pdbsum/2y5m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y5m 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=2y5m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2y5m OCA], [https://pdbe.org/2y5m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2y5m RCSB], [https://www.ebi.ac.uk/pdbsum/2y5m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2y5m ProSAT]</span></td></tr> |
| | </table> | | </table> |
| Line 27: |
Line 26: |
| | [[Category: Brevibacillus brevis]] | | [[Category: Brevibacillus brevis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Aragao, D]] | + | [[Category: Aragao D]] |
| - | [[Category: Caffrey, M]] | + | [[Category: Caffrey M]] |
| - | [[Category: Hoefer, N]] | + | [[Category: Hoefer N]] |
| - | [[Category: Antibiotic]]
| + | |
| - | [[Category: Ion channel]]
| + | |
| - | [[Category: Mesophase]]
| + | |
| - | [[Category: Sponge phase]]
| + | |
| Structural highlights
2y5m is a 6 chain structure with sequence from Brevibacillus brevis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Method: | X-ray diffraction, Resolution 1.08Å |
| Ligands: | , , , , , |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
Gramicidin is an apolar pentadecapeptide antibiotic consisting of alternating D-and L-amino acids. It functions, in part, by creating pores in membranes of susceptible cells rendering them leaky to monovalent cations. The peptide should be able to traverse the host membrane either as a double stranded, intertwined double helix (DSDH) or as a head-to-head single stranded helix (HHSH). Current structure models are based on macromolecular X-ray crystallography (MX) and nuclear magnetic resonance (NMR). However, the HHSH form has only been observed by NMR. The shape and size of the different gramicidin conformations differ. We speculated therefore that reconstituting it into a lipidic mesophase with bilayers of different microstructures would preferentially stabilize one form over the other. By using such mesophases for in meso crystallogenesis the expectation was that at least one would generate crystals of gramicidin in the HHSH form for structure determination by MX. This was tested using commercial and in-house synthesised lipids that support in meso crystallogenesis. Lipid acyl chain lengths were varied from 14 to 18 carbons to provide mesophases with a range of bilayer thicknesses. Unexpectedly, all lipids produced high quality, structure-grade crystals with gramicidin only in the DSDH conformation.
Membrane Protein Crystallization in Lipidic Mesophases. Hosting lipid affects on the crystallization and structure of a transmembrane peptide.,Hofer N, Aragao D, Lyons JA, Caffrey M Cryst Growth Des. 2011 Apr 6;11(4):1182-1192. Epub 2011 Feb 16. PMID:22933857[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Hofer N, Aragao D, Lyons JA, Caffrey M. Membrane Protein Crystallization in Lipidic Mesophases. Hosting lipid affects on the crystallization and structure of a transmembrane peptide. Cryst Growth Des. 2011 Apr 6;11(4):1182-1192. Epub 2011 Feb 16. PMID:22933857 doi:http://dx.doi.org/10.1021/cg101384p
|
