6ga3: Difference between revisions
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The | ==Bacteriorhodopsin, 33 ms state, ensemble refinement== | ||
<StructureSection load='6ga3' size='340' side='right'caption='[[6ga3]], [[Resolution|resolution]] 2.10Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6ga3]] 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=6GA3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6GA3 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=C14:TETRADECANE'>C14</scene>, <scene name='pdbligand=D10:DECANE'>D10</scene>, <scene name='pdbligand=DD9:NONANE'>DD9</scene>, <scene name='pdbligand=HP6:HEPTANE'>HP6</scene>, <scene name='pdbligand=L2P:2,3-DI-PHYTANYL-GLYCEROL'>L2P</scene>, <scene name='pdbligand=MYS:PENTADECANE'>MYS</scene>, <scene name='pdbligand=OCT:N-OCTANE'>OCT</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene>, <scene name='pdbligand=TRD:TRIDECANE'>TRD</scene>, <scene name='pdbligand=UND:UNDECANE'>UND</scene></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=6ga3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ga3 OCA], [https://pdbe.org/6ga3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ga3 RCSB], [https://www.ebi.ac.uk/pdbsum/6ga3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ga3 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA] Light-driven proton pump. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Bacteriorhodopsin (bR) is a light-driven proton pump. The primary photochemical event upon light absorption is isomerization of the retinal chromophore. Here we used time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy were used to identify a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multiphoton effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins. | |||
Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin.,Nass Kovacs G, Colletier JP, Grunbein ML, Yang Y, Stensitzki T, Batyuk A, Carbajo S, Doak RB, Ehrenberg D, Foucar L, Gasper R, Gorel A, Hilpert M, Kloos M, Koglin JE, Reinstein J, Roome CM, Schlesinger R, Seaberg M, Shoeman RL, Stricker M, Boutet S, Haacke S, Heberle J, Heyne K, Domratcheva T, Barends TRM, Schlichting I Nat Commun. 2019 Jul 18;10(1):3177. doi: 10.1038/s41467-019-10758-0. PMID:31320619<ref>PMID:31320619</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6ga3" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: | ==See Also== | ||
[[Category: | *[[Bacteriorhodopsin 3D structures|Bacteriorhodopsin 3D structures]] | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
[[Category: | __TOC__ | ||
[[Category: | </StructureSection> | ||
[[Category: | [[Category: Halobacterium salinarum NRC-1]] | ||
[[Category: Gasper | [[Category: Large Structures]] | ||
[[Category: | [[Category: Barends TRM]] | ||
[[Category: | [[Category: Batyuk A]] | ||
[[Category: | [[Category: Boutet S]] | ||
[[Category: | [[Category: Carbajo S]] | ||
[[Category: | [[Category: Colletier J-P]] | ||
[[Category: | [[Category: Doak RB]] | ||
[[Category: | [[Category: Domratcheva T]] | ||
[[Category: | [[Category: Ehrenberg D]] | ||
[[Category: | [[Category: Foucar L]] | ||
[[Category: | [[Category: Gasper R]] | ||
[[Category: | [[Category: Gorel A]] | ||
[[Category: | [[Category: Gruenbein ML]] | ||
[[Category: | [[Category: Haacke S]] | ||
[[Category: | [[Category: Heberle J]] | ||
[[Category: Stensitzki | [[Category: Hilpert M]] | ||
[[Category: Kloos M]] | |||
[[Category: Koglin J]] | |||
[[Category: Nass Kovacs G]] | |||
[[Category: Reinstein J]] | |||
[[Category: Roome CM]] | |||
[[Category: Schlesinger R]] | |||
[[Category: Schlichting I]] | |||
[[Category: Seaberg M]] | |||
[[Category: Shoeman RL]] | |||
[[Category: Stensitzki T]] | |||
[[Category: Stricker M]] | |||
Latest revision as of 10:58, 17 October 2024
Bacteriorhodopsin, 33 ms state, ensemble refinementBacteriorhodopsin, 33 ms state, ensemble refinement
Structural highlights
FunctionBACR_HALSA Light-driven proton pump. Publication Abstract from PubMedBacteriorhodopsin (bR) is a light-driven proton pump. The primary photochemical event upon light absorption is isomerization of the retinal chromophore. Here we used time-resolved crystallography at an X-ray free-electron laser to follow the structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds. Quantum chemistry and ultrafast spectroscopy were used to identify a sequential two-photon absorption process, leading to excitation of a tryptophan residue flanking the retinal chromophore, as a first manifestation of multiphoton effects. We resolve distinct stages in the structural dynamics of the all-trans retinal in photoexcited bR to a highly twisted 13-cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions of the electronically excited retinal chromophore, the surrounding amino acids and water molecules as well as their hydrogen bonding network. These results show that this extended photo-active network forms an electronically and vibrationally coupled system in bR, and most likely in all retinal proteins. Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin.,Nass Kovacs G, Colletier JP, Grunbein ML, Yang Y, Stensitzki T, Batyuk A, Carbajo S, Doak RB, Ehrenberg D, Foucar L, Gasper R, Gorel A, Hilpert M, Kloos M, Koglin JE, Reinstein J, Roome CM, Schlesinger R, Seaberg M, Shoeman RL, Stricker M, Boutet S, Haacke S, Heberle J, Heyne K, Domratcheva T, Barends TRM, Schlichting I Nat Commun. 2019 Jul 18;10(1):3177. doi: 10.1038/s41467-019-10758-0. PMID:31320619[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCACategories:
- Halobacterium salinarum NRC-1
- Large Structures
- Barends TRM
- Batyuk A
- Boutet S
- Carbajo S
- Colletier J-P
- Doak RB
- Domratcheva T
- Ehrenberg D
- Foucar L
- Gasper R
- Gorel A
- Gruenbein ML
- Haacke S
- Heberle J
- Hilpert M
- Kloos M
- Koglin J
- Nass Kovacs G
- Reinstein J
- Roome CM
- Schlesinger R
- Schlichting I
- Seaberg M
- Shoeman RL
- Stensitzki T
- Stricker M