5j7a: Difference between revisions

Latest revision as of 10:51, 6 September 2023

Bacteriorhodopsin ground state structure obtained with Serial Femtosecond Crystallography

Structural highlights

5j7a is a 1 chain structure with sequence from Halobacterium salinarum NRC-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.3Å
Ligands:	LI1, RET
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

BACR_HALSA Light-driven proton pump.

Publication Abstract from PubMed

Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 A resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.

Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography.,Nogly P, Panneels V, Nelson G, Gati C, Kimura T, Milne C, Milathianaki D, Kubo M, Wu W, Conrad C, Coe J, Bean R, Zhao Y, Bath P, Dods R, Harimoorthy R, Beyerlein KR, Rheinberger J, James D, DePonte D, Li C, Sala L, Williams GJ, Hunter MS, Koglin JE, Berntsen P, Nango E, Iwata S, Chapman HN, Fromme P, Frank M, Abela R, Boutet S, Barty A, White TA, Weierstall U, Spence J, Neutze R, Schertler G, Standfuss J Nat Commun. 2016 Aug 22;7:12314. doi: 10.1038/ncomms12314. PMID:27545823^[1]

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

References

↑ Nogly P, Panneels V, Nelson G, Gati C, Kimura T, Milne C, Milathianaki D, Kubo M, Wu W, Conrad C, Coe J, Bean R, Zhao Y, Bath P, Dods R, Harimoorthy R, Beyerlein KR, Rheinberger J, James D, DePonte D, Li C, Sala L, Williams GJ, Hunter MS, Koglin JE, Berntsen P, Nango E, Iwata S, Chapman HN, Fromme P, Frank M, Abela R, Boutet S, Barty A, White TA, Weierstall U, Spence J, Neutze R, Schertler G, Standfuss J. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography. Nat Commun. 2016 Aug 22;7:12314. doi: 10.1038/ncomms12314. PMID:27545823 doi:https://dx.doi.org/10.1038/ncomms12314

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Nogly P, Panneels V, Nelson G, Gati C, Kimura T, Milne C, Milathianaki D, Kubo M, Wu W, Conrad C, Coe J, Bean R, Zhao Y, Bath P, Dods R, Harimoorthy R, Beyerlein KR, Rheinberger J, James D, DePonte D, Li C, Sala L, Williams GJ, Hunter MS, Koglin JE, Berntsen P, Nango E, Iwata S, Chapman HN, Fromme P, Frank M, Abela R, Boutet S, Barty A, White TA, Weierstall U, Spence J, Neutze R, Schertler G, Standfuss J. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography. Nat Commun. 2016 Aug 22;7:12314. doi: 10.1038/ncomms12314. PMID:27545823 doi:https://dx.doi.org/10.1038/ncomms12314

[1]

@@ Line 1: / Line 1: @@
 ==Bacteriorhodopsin ground state structure obtained with Serial Femtosecond Crystallography==
-<StructureSection load='5j7a' size='340' side='right' caption='[[5j7a]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='5j7a' size='340' side='right'caption='[[5j7a]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5j7a]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Halsa Halsa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J7A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5J7A FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5j7a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Halobacterium_salinarum_NRC-1 Halobacterium salinarum NRC-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J7A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J7A FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=LI1:1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL'>LI1</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]] 2.3&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">bop, VNG_1467G ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=64091 HALSA])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LI1:1-[2,6,10.14-TETRAMETHYL-HEXADECAN-16-YL]-2-[2,10,14-TRIMETHYLHEXADECAN-16-YL]GLYCEROL'>LI1</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=5j7a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j7a OCA], [http://pdbe.org/5j7a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j7a RCSB], [http://www.ebi.ac.uk/pdbsum/5j7a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j7a 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=5j7a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j7a OCA], [https://pdbe.org/5j7a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j7a RCSB], [https://www.ebi.ac.uk/pdbsum/5j7a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j7a ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.
+[https://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA] Light-driven proton pump.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 19: / Line 19: @@
 </div>
 <div class="pdbe-citations 5j7a" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Halsa]]
+[[Category: Halobacterium salinarum NRC-1]]
-[[Category: Abela, R]]
+[[Category: Large Structures]]
-[[Category: Barty, A]]
+[[Category: Abela R]]
-[[Category: Bath, P]]
+[[Category: Barty A]]
-[[Category: Bean, R]]
+[[Category: Bath P]]
-[[Category: Berntsen, P]]
+[[Category: Bean R]]
-[[Category: Beyerlein, K R]]
+[[Category: Berntsen P]]
-[[Category: Boutet, S]]
+[[Category: Beyerlein KR]]
-[[Category: Chapman, H N]]
+[[Category: Boutet S]]
-[[Category: Coe, J]]
+[[Category: Chapman HN]]
-[[Category: Conrad, C]]
+[[Category: Coe J]]
-[[Category: DePonte, D]]
+[[Category: Conrad C]]
-[[Category: Dods, R]]
+[[Category: DePonte D]]
-[[Category: Frank, M]]
+[[Category: Dods R]]
-[[Category: Fromme, P]]
+[[Category: Frank M]]
-[[Category: Gati, C]]
+[[Category: Fromme P]]
-[[Category: Harimoorthy, R]]
+[[Category: Gati C]]
-[[Category: Hunter, M]]
+[[Category: Harimoorthy R]]
-[[Category: Iwata, S]]
+[[Category: Hunter M]]
-[[Category: James, D]]
+[[Category: Iwata S]]
-[[Category: Kimura, T]]
+[[Category: James D]]
-[[Category: Koglin, J E]]
+[[Category: Kimura T]]
-[[Category: Kubo, M]]
+[[Category: Koglin JE]]
-[[Category: Li, C]]
+[[Category: Kubo M]]
-[[Category: Milathianaki, D]]
+[[Category: Li C]]
-[[Category: Milne, C]]
+[[Category: Milathianaki D]]
-[[Category: Nango, E]]
+[[Category: Milne C]]
-[[Category: Nelson, G]]
+[[Category: Nango E]]
-[[Category: Neutze, R]]
+[[Category: Nelson G]]
-[[Category: Nogly, P]]
+[[Category: Neutze R]]
-[[Category: Panneels, V]]
+[[Category: Nogly P]]
-[[Category: Rheinberger, J]]
+[[Category: Panneels V]]
-[[Category: Sala, L]]
+[[Category: Rheinberger J]]
-[[Category: Schertler, G]]
+[[Category: Sala L]]
-[[Category: Spence, J]]
+[[Category: Schertler G]]
-[[Category: Standfuss, J]]
+[[Category: Spence J]]
-[[Category: Weierstall, U]]
+[[Category: Standfuss J]]
-[[Category: White, T A]]
+[[Category: Weierstall U]]
-[[Category: Williams, G]]
+[[Category: White TA]]
-[[Category: Wu, W]]
+[[Category: Williams G]]
-[[Category: Zhao, Y]]
+[[Category: Wu W]]
-[[Category: Light-driven proton pump]]
+[[Category: Zhao Y]]
-[[Category: Proton transport]]
-[[Category: Retinal binding]]
-[[Category: Seven transmembrane helix protein]]

5j7a: Difference between revisions

Latest revision as of 10:51, 6 September 2023

Bacteriorhodopsin ground state structure obtained with Serial Femtosecond Crystallography

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Page actions

Page actions

Personal tools

Navigation

Search

Tools