6GA2

Bacteriorhodopsin, dark state, cell 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

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:  
    6GAI, 6GAH, 6GAA, 6GAC, 6GAB, 6GAE, 6GAD, 6GAG, 6GAF, 6GA9

  • 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
BacteriorhodopsinA249Halobacterium 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 10 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
L2P
Query on L2P

Download Ideal Coordinates CCD File 
C [auth A], K [auth A], L [auth A]2,3-DI-PHYTANYL-GLYCEROL
C43 H88 O3
ISDBCJSGCHUHFI-UMZPFTBHSA-N
 Ligand Interaction
RET
Query on RET

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B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
MYS
Query on MYS

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I [auth A]PENTADECANE
C15 H32
YCOZIPAWZNQLMR-UHFFFAOYSA-N
 Ligand Interaction
C14
Query on C14

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N [auth A]TETRADECANE
C14 H30
BGHCVCJVXZWKCC-UHFFFAOYSA-N
 Ligand Interaction
TRD
Query on TRD

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D [auth A]TRIDECANE
C13 H28
IIYFAKIEWZDVMP-UHFFFAOYSA-N
 Ligand Interaction
UND
Query on UND

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J [auth A], P [auth A]UNDECANE
C11 H24
RSJKGSCJYJTIGS-UHFFFAOYSA-N
 Ligand Interaction
D10
Query on D10

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E [auth A]DECANE
C10 H22
DIOQZVSQGTUSAI-UHFFFAOYSA-N
 Ligand Interaction
DD9
Query on DD9

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M [auth A]nonane
C9 H20
BKIMMITUMNQMOS-UHFFFAOYSA-N
 Ligand Interaction
OCT
Query on OCT

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G [auth A], H [auth A], O [auth A]N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
HP6
Query on HP6

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F [auth A]HEPTANE
C7 H16
IMNFDUFMRHMDMM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • 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

View Full Validation Report



Entry History & Funding Information

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references