6RMK

Bacteriorhodopsin, dark state, cell 2, refined using the same protocol as sub-ps time delays


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin.

Nass Kovacs, G.Colletier, J.P.Grunbein, M.L.Yang, Y.Stensitzki, T.Batyuk, A.Carbajo, S.Doak, R.B.Ehrenberg, D.Foucar, L.Gasper, R.Gorel, A.Hilpert, M.Kloos, M.Koglin, J.E.Reinstein, J.Roome, C.M.Schlesinger, R.Seaberg, M.Shoeman, R.L.Stricker, M.Boutet, S.Haacke, S.Heberle, J.Heyne, K.Domratcheva, T.Barends, T.R.M.Schlichting, I.

(2019) Nat Commun 10: 3177-3177

  • DOI: 10.1038/s41467-019-10758-0
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • 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 structur ...

    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.


    Organizational Affiliation

    Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA, 94025, USA.,Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany. Tatjana.Domratcheva@mpimf-heidelberg.mpg.de.,Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, 71 Avenue des Martyrs, 38000, Grenoble, France.,Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany.,Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.,Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany. Ilme.Schlichting@mpimf-heidelberg.mpg.de.,Université de Strasbourg-CNRS, UMR 7504, IPCMS, 23 Rue du Loess, 67034, Strasbourg, France.,Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195, Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Bacteriorhodopsin
A
231Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)Mutation(s): 0 
Gene Names: bop
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Go to UniProtKB:  P02945
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download SDF File 
Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.243 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 62.100α = 90.00
b = 62.100β = 90.00
c = 110.500γ = 120.00
Software Package:
Software NamePurpose
CrystFELdata reduction
PHASERphasing
PHENIXrefinement
CrystFELdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2019-06-05
    Type: Initial release
  • Version 1.1: 2019-07-31
    Type: Data collection, Database references