L intermediate of bacteriorhodopsin

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 

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Helix Deformation is Coupled to Vectorial Proton Transport in Bacteriorhodopsin'S Photocycle

Royant, A.Edman, K.Ursby, T.Pebay-Peyroula, E.Landau, E.M.Neutze, R.

(2000) Nature 406: 645

  • DOI: https://doi.org/10.1038/35020599
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    A wide variety of mechanisms are used to generate a proton-motive potential across cell membranes, a function lying at the heart of bioenergetics. Bacteriorhodopsin, the simplest known proton pump, provides a paradigm for understanding this process. Here we report, at 2.1 A resolution, the structural changes in bacteriorhodopsin immediately preceding the primary proton transfer event in its photocycle. The early structural rearrangements propagate from the protein's core towards the extracellular surface, disrupting the network of hydrogen-bonded water molecules that stabilizes helix C in the ground state. Concomitantly, a bend of this helix enables the negatively charged primary proton acceptor, Asp 85, to approach closer to the positively charged primary proton donor, the Schiff base. The primary proton transfer event would then neutralize these two groups, cancelling their electrostatic attraction and facilitating a relaxation of helix C to a less strained geometry. Reprotonation of the Schiff base by Asp 85 would thereby be impeded, ensuring vectorial proton transport. Structural rearrangements also occur near the protein's surface, aiding proton release to the extracellular medium.

  • Organizational Affiliation

    Institut de Biologie Structurale, CEA-CNRS-Université Joseph Fourier, UMR 5075, Grenoble, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
BACTERIORHODOPSIN, GROUND STATE228Halobacterium salinarumMutation(s): 0 
Membrane Entity: Yes 
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02945
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on RET

Download Ideal Coordinates CCD File 
C20 H28 O
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.265 
  • R-Value Observed: 0.265 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.96α = 90
b = 60.96β = 90
c = 109.97γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata scaling
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance