6RMK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    6GA1, 6GA2, 6GA3, 6GA4, 6GA5, 6GA6, 6GA7, 6GA8, 6GA9, 6GAA, 6GAB, 6GAC, 6GAD, 6GAE, 6GAF, 6GAG, 6GAH, 6GAI, 6RMK

  • 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 structural changes in multiphoton-excited bR from 250 femtoseconds to 10 picoseconds ...

    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

    Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120, Heidelberg, Germany. Ilme.Schlichting@mpimf-heidelberg.mpg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BacteriorhodopsinA231Halobacterium salinarum NRC-1Mutation(s): 0 
Gene Names: bopVNG_1467G
Membrane Entity: Yes 
UniProt
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET (Subject of Investigation/LOI)
Query on RET

Download Ideal Coordinates CCD File 
B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.244 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.1α = 90
b = 62.1β = 90
c = 110.5γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

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