1QKO

HIGH RESOLUTION X-RAY STRUCTURE OF AN EARLY INTERMEDIATE IN THE BACTERIORHODOPSIN PHOTOCYCLE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

High Resolution X-Ray Structure of an Early Intermediate in the Bacteriorhodopsin Photocycle

Edman, K.Nollert, P.Royant, A.Belrhali, H.Pebay-Peyroula, E.Hajdu, J.Neutze, R.Landau, E.M.

(1999) Nature 401: 822

  • DOI: 10.1038/44623
  • Primary Citation of Related Structures:  
    1QKP, 1QKO

  • PubMed Abstract: 
  • Bacteriorhodopsin is the simplest known photon-driven proton pump and as such provides a model for the study of a basic function in bioenergetics. Its seven transmembrane helices encompass a proton translocation pathway containing the chromophore, a retinal molecule covalently bound to lysine 216 through a protonated Schiff base, and a series of proton donors and acceptors ...

    Bacteriorhodopsin is the simplest known photon-driven proton pump and as such provides a model for the study of a basic function in bioenergetics. Its seven transmembrane helices encompass a proton translocation pathway containing the chromophore, a retinal molecule covalently bound to lysine 216 through a protonated Schiff base, and a series of proton donors and acceptors. Photoisomerization of the all-trans retinal to the 13-cis configuration initiates the vectorial translocation of a proton from the Schiff base, the primary proton donor, to the extracellular side, followed by reprotonation of the Schiff base from the cytoplasm. Here we describe the high-resolution X-ray structure of an early intermediate in the photocycle of bacteriorhodopsin, which is formed directly after photoexcitation. A key water molecule is dislocated, allowing the primary proton acceptor, Asp 85, to move. Movement of the main-chain Lys 216 locally disrupts the hydrogen-bonding network of helix G, facilitating structural changes later in the photocycle.


    Related Citations: 
    • Protein, Lipid and Water Organization in Bacteriorhodopsin: A Molecular View of the Purple Membrane at 1.9 Angstrom Resolution
      Belrhali, H., Nollert, P., Royant, A., Menzel, C., Rosenbusch, J.P., Landau, E.M., Pebay-Peyroula, E.
      (1999) Structure 7: 909

    Organizational Affiliation

    Department of Biochemistry, Uppsala University, Biomedical Centre, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BACTERIORHODOPSIN A248Halobacterium salinarumMutation(s): 0 
Membrane protein
Mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial, Algal, Viral, and Unusual Rhodopsins
Protein: 
Bacteriorhodopsin (BR), K intermediate
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
Query on RET

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.06α = 90
b = 61.06β = 90
c = 110.57γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CCP4data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-15
    Changes: Data collection, Derived calculations, Experimental preparation, Other