5itc: Difference between revisions

Latest revision as of 14:08, 30 August 2023

2.2-Angstrom in meso crystal structure of Haloquadratum Walsbyi Bacteriorhodopsin (HwBR) from Styrene Maleic Acid (SMA) Polymer Nanodiscs

Structural highlights

5itc is a 3 chain structure with sequence from Haloquadratum walsbyi DSM 16790. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.999Å
Ligands:	OLB, OLC, RET
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BACR1_HALWD Light-driven proton pump. The chromophore contains 78% all-trans- and 22% 13-cis-retinal in the dark and 90% all-trans- and 10% 13-cis-retinal upon illumination with >500 nm light.^[1] ^[2] ^[3]

Publication Abstract from PubMed

For some membrane proteins, detergent-mediated solubilization compromises protein stability and functionality, often impairing biophysical and structural analyses. Hence, membrane-protein structure determination is a continuing bottleneck in the field of protein crystallography. Here, as an alternative to approaches mediated by conventional detergents, we report the crystallogenesis of a recombinantly produced membrane protein that never left a lipid bilayer environment. We used styrene-maleic acid (SMA) copolymers to solubilize lipid-embedded proteins into SMA nanodiscs, purified these discs by affinity and size-exclusion chromatography, and transferred proteins into the lipidic cubic phase (LCP) for in meso crystallization. The 2.0-A structure of an alpha-helical seven-transmembrane microbial rhodopsin thus obtained is of high quality and virtually identical to the 2.2-A structure obtained from traditional detergent-based purification and subsequent LCP crystallization.

Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs.,Broecker J, Eger BT, Ernst OP Structure. 2017 Jan 3. pii: S0969-2126(16)30394-X. doi:, 10.1016/j.str.2016.12.004. PMID:28089451^[4]

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

References

↑ Sudo Y, Ihara K, Kobayashi S, Suzuki D, Irieda H, Kikukawa T, Kandori H, Homma M. A microbial rhodopsin with a unique retinal composition shows both sensory rhodopsin II and bacteriorhodopsin-like properties. J Biol Chem. 2011 Feb 25;286(8):5967-76. doi: 10.1074/jbc.M110.190058. Epub 2010 , Dec 6. PMID:21135094 doi:https://dx.doi.org/10.1074/jbc.M110.190058
↑ Lobasso S, Lopalco P, Vitale R, Saponetti MS, Capitanio G, Mangini V, Milano F, Trotta M, Corcelli A. The light-activated proton pump Bop I of the archaeon Haloquadratum walsbyi. Photochem Photobiol. 2012 May-Jun;88(3):690-700. doi:, 10.1111/j.1751-1097.2012.01089.x. Epub 2012 Feb 9. PMID:22248212 doi:https://dx.doi.org/10.1111/j.1751-1097.2012.01089.x
↑ Sudo Y, Okazaki A, Ono H, Yagasaki J, Sugo S, Kamiya M, Reissig L, Inoue K, Ihara K, Kandori H, Takagi S, Hayashi S. A blue-shifted light-driven proton pump for neural silencing. J Biol Chem. 2013 Jul 12;288(28):20624-32. doi: 10.1074/jbc.M113.475533. Epub, 2013 May 28. PMID:23720753 doi:https://dx.doi.org/10.1074/jbc.M113.475533
↑ Broecker J, Eger BT, Ernst OP. Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs. Structure. 2017 Jan 3. pii: S0969-2126(16)30394-X. doi:, 10.1016/j.str.2016.12.004. PMID:28089451 doi:https://dx.doi.org/10.1016/j.str.2016.12.004

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OCA

[1] Sudo Y, Ihara K, Kobayashi S, Suzuki D, Irieda H, Kikukawa T, Kandori H, Homma M. A microbial rhodopsin with a unique retinal composition shows both sensory rhodopsin II and bacteriorhodopsin-like properties. J Biol Chem. 2011 Feb 25;286(8):5967-76. doi: 10.1074/jbc.M110.190058. Epub 2010 , Dec 6. PMID:21135094 doi:https://dx.doi.org/10.1074/jbc.M110.190058

[2] Lobasso S, Lopalco P, Vitale R, Saponetti MS, Capitanio G, Mangini V, Milano F, Trotta M, Corcelli A. The light-activated proton pump Bop I of the archaeon Haloquadratum walsbyi. Photochem Photobiol. 2012 May-Jun;88(3):690-700. doi:, 10.1111/j.1751-1097.2012.01089.x. Epub 2012 Feb 9. PMID:22248212 doi:https://dx.doi.org/10.1111/j.1751-1097.2012.01089.x

[3] Sudo Y, Okazaki A, Ono H, Yagasaki J, Sugo S, Kamiya M, Reissig L, Inoue K, Ihara K, Kandori H, Takagi S, Hayashi S. A blue-shifted light-driven proton pump for neural silencing. J Biol Chem. 2013 Jul 12;288(28):20624-32. doi: 10.1074/jbc.M113.475533. Epub, 2013 May 28. PMID:23720753 doi:https://dx.doi.org/10.1074/jbc.M113.475533

[4] Broecker J, Eger BT, Ernst OP. Crystallogenesis of Membrane Proteins Mediated by Polymer-Bounded Lipid Nanodiscs. Structure. 2017 Jan 3. pii: S0969-2126(16)30394-X. doi:, 10.1016/j.str.2016.12.004. PMID:28089451 doi:https://dx.doi.org/10.1016/j.str.2016.12.004

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[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==2.2-Angstrom in meso crystal structure of Haloquadratum Walsbyi Bacteriorhodopsin (HwBR) from Styrene Maleic Acid (SMA) Polymer Nanodiscs==
-<StructureSection load='5itc' size='340' side='right' caption='[[5itc]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+<StructureSection load='5itc' size='340' side='right'caption='[[5itc]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5itc]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ITC OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ITC FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5itc]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Haloquadratum_walsbyi_DSM_16790 Haloquadratum walsbyi DSM 16790]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ITC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ITC FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=OLB:(2S)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLB</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=RET:RETINAL'>RET</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]] 1.999&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5ite|5ite]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=OLB:(2S)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLB</scene>, <scene name='pdbligand=OLC:(2R)-2,3-DIHYDROXYPROPYL+(9Z)-OCTADEC-9-ENOATE'>OLC</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></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=5itc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5itc OCA], [http://pdbe.org/5itc PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5itc RCSB], [http://www.ebi.ac.uk/pdbsum/5itc PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5itc 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=5itc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5itc OCA], [https://pdbe.org/5itc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5itc RCSB], [https://www.ebi.ac.uk/pdbsum/5itc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5itc ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/BACR1_HALWD BACR1_HALWD]] Light-driven proton pump. The chromophore contains 78% all-trans- and 22% 13-cis-retinal in the dark and 90% all-trans- and 10% 13-cis-retinal upon illumination with >500 nm light.<ref>PMID:21135094</ref> <ref>PMID:22248212</ref> <ref>PMID:23720753</ref>
+[https://www.uniprot.org/uniprot/BACR1_HALWD BACR1_HALWD] Light-driven proton pump. The chromophore contains 78% all-trans- and 22% 13-cis-retinal in the dark and 90% all-trans- and 10% 13-cis-retinal upon illumination with >500 nm light.<ref>PMID:21135094</ref> <ref>PMID:22248212</ref> <ref>PMID:23720753</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5itc" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Broecker, J]]
+[[Category: Haloquadratum walsbyi DSM 16790]]
-[[Category: Eger, B T]]
+[[Category: Large Structures]]
-[[Category: Ernst, O P]]
+[[Category: Broecker J]]
-[[Category: Bacteriorhodopsin from haloquadratum walsbyi]]
+[[Category: Eger BT]]
-[[Category: Detergent-free]]
+[[Category: Ernst OP]]
-[[Category: Lipidic cubic phase]]
-[[Category: Membrane protein]]

5itc: Difference between revisions

Latest revision as of 14:08, 30 August 2023

2.2-Angstrom in meso crystal structure of Haloquadratum Walsbyi Bacteriorhodopsin (HwBR) from Styrene Maleic Acid (SMA) Polymer Nanodiscs

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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