5kkh: Difference between revisions

Latest revision as of 10:02, 27 September 2023

2.1-Angstrom In situ Mylar structure of bacteriorhodopsin from Haloquadratum walsbyi (HwBR) at 100 K

Structural highlights

5kkh 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 2.125Å
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

In recent years, in situ data collection has been a major focus of progress in protein crystallography. Here, we introduce the Mylar in situ method using Mylar-based sandwich plates that are inexpensive, easy to make and handle, and show significantly less background scattering than other setups. A variety of cognate holders for patches of Mylar in situ sandwich films corresponding to one or more wells makes the method robust and versatile, allows for storage and shipping of entire wells, and enables automated crystal imaging, screening, and goniometer-based X-ray diffraction data-collection at room temperature and under cryogenic conditions for soluble and membrane-protein crystals grown in or transferred to these plates. We validated the Mylar in situ method using crystals of the water-soluble proteins hen egg-white lysozyme and sperm whale myoglobin as well as the 7-transmembrane protein bacteriorhodopsin from Haloquadratum walsbyi. In conjunction with current developments at synchrotrons, this approach promises high-resolution structural studies of membrane proteins to become faster and more routine.

A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals.,Broecker J, Klingel V, Ou WL, Balo AR, Kissick DJ, Ogata CM, Kuo A, Ernst OP Cryst Growth Des. 2016 Nov 2;16(11):6318-6326. doi: 10.1021/acs.cgd.6b00950. Epub, 2016 Oct 3. PMID:28261000^[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, Klingel V, Ou WL, Balo AR, Kissick DJ, Ogata CM, Kuo A, Ernst OP. A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals. Cryst Growth Des. 2016 Nov 2;16(11):6318-6326. doi: 10.1021/acs.cgd.6b00950. Epub, 2016 Oct 3. PMID:28261000 doi:https://dx.doi.org/10.1021/acs.cgd.6b00950

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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, Klingel V, Ou WL, Balo AR, Kissick DJ, Ogata CM, Kuo A, Ernst OP. A Versatile System for High-Throughput In Situ X-ray Screening and Data Collection of Soluble and Membrane-Protein Crystals. Cryst Growth Des. 2016 Nov 2;16(11):6318-6326. doi: 10.1021/acs.cgd.6b00950. Epub, 2016 Oct 3. PMID:28261000 doi:https://dx.doi.org/10.1021/acs.cgd.6b00950

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[2]

[3]

[4]

@@ Line 1: / Line 1: @@
 ==2.1-Angstrom In situ Mylar structure of bacteriorhodopsin from Haloquadratum walsbyi (HwBR) at 100 K==
-<StructureSection load='5kkh' size='340' side='right' caption='[[5kkh]], [[Resolution|resolution]] 2.12&Aring;' scene=''>
+<StructureSection load='5kkh' size='340' side='right'caption='[[5kkh]], [[Resolution|resolution]] 2.12&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5kkh]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Halwd Halwd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5KKH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KKH FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5kkh]] 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=5KKH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KKH 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]] 2.125&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5kki|5kki]], [[5kkj|5kkj]], [[5kkk|5kkk]]</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='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bop1, bopI, HQ_1014A ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=362976 HALWD])</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=5kkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kkh OCA], [https://pdbe.org/5kkh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5kkh RCSB], [https://www.ebi.ac.uk/pdbsum/5kkh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5kkh 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=5kkh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5kkh OCA], [http://pdbe.org/5kkh PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5kkh RCSB], [http://www.ebi.ac.uk/pdbsum/5kkh PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5kkh 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 22: / Line 21: @@
 ==See Also==
-*[[Bacteriorhodopsin|Bacteriorhodopsin]]
+*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Halwd]]
+[[Category: Haloquadratum walsbyi DSM 16790]]
-[[Category: Broecker, J]]
+[[Category: Large Structures]]
-[[Category: Ernst, O P]]
+[[Category: Broecker J]]
-[[Category: Membrane protein]]
+[[Category: Ernst OP]]
-[[Category: Transport protein]]

5kkh: Difference between revisions

Latest revision as of 10:02, 27 September 2023

2.1-Angstrom In situ Mylar structure of bacteriorhodopsin from Haloquadratum walsbyi (HwBR) at 100 K

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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