Experimental Data Snapshot

  • Resolution: 3.50 Å
  • R-Value Work: 0.280 

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history


Electron-crystallographic refinement of the structure of bacteriorhodopsin.

Grigorieff, N.Ceska, T.A.Downing, K.H.Baldwin, J.M.Henderson, R.

(1996) J Mol Biol 259: 393-421

  • DOI: 10.1006/jmbi.1996.0328
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Using electron diffraction data corrected for diffuse scattering together with additional phase information from 30 new images of tilted specimens, an improved experimental density map has been calculated for bacteriorhodopsin. The atomic model has t ...

    Using electron diffraction data corrected for diffuse scattering together with additional phase information from 30 new images of tilted specimens, an improved experimental density map has been calculated for bacteriorhodopsin. The atomic model has then been rebuilt into this new map with particular attention to the surface loops. All the residues from 7 to 227 as well as ten lipid molecules are now included, although a few amino acid residues in three of the six surface loops, about half of the lipid hydrophobic chains and all of the lipid head groups are disordered. The model has then been refined against the experimental diffraction amplitudes to an R-factor of 28% at 3.5 angstrom resolution with strict geometry (0.005 angstrom) bond length deviation) using the improvement of the "free" phase residual between calculated and experimental phases from images as an objective criterion of accuracy. For the refinement some new programs were developed to restrain the number of parameters, to be compatible with the limited resolution of our data. In the final refined model of the protein (2BRD), compared with earlier co-ordinates (1BRD), helix D has been moved towards the cytoplasm by almost 4 angstrom, and the overall accuracy of the co-ordinates of residues in the other six helices has been improved. As a result the positions of nearly all the important residues in bacteriorhodopsin are now well determined. In particular, the buried, protonated Asp115 is 7 angstrom from, and so not in contact with, the retinal and Met118 forms a cap on the pocket occupied by the beta-ionone ring. No clear density exists for the side-chain of Arg82, which forms a central part of the extracellular half-channel. The only arginine side-chain built into good density is that of Arg134 at the extracellular end of helix E, the others being disordered near one of the two surfaces. The interpretation of the end of helix F on the extracellular surface is now clearer; an extra loose helical turn has been built bringing the side-chain of Glu194 close to Arg134 to form a probable salt bridge. The model provides an improved framework for understanding the mechanism of the light-driven proton pumping. A number of cavities that could contain water molecules were found by searching the refined model, most of them above or below the Schiff base in the half-channels leading to the two surfaces. The ordered and disordered regions of the structure are described by the temperature factor distribution.

    Related Citations: 
    • Analysis of High-Resolution Electron Diffraction Patterns from Purple Membrane Labelled with Heavy-Atoms
      Ceska, T.A., Henderson, R.
      (1990) J Mol Biol 213: 539
    • Model for the Structure of Bacteriorhodopsin Based on High-Resolution Electron Cryo-Microscopy
      Henderson, R., Baldwin, J.M., Ceska, T.A., Zemlin, F., Beckmann, E., Downing, K.H.
      (1990) J Mol Biol 213: 899
    • Three-Dimensional Model of Purple Membrane Obtained by Electron Microscopy
      Henderson, R., Unwin, P.N.
      (1975) Nature 257: 28

    Organizational Affiliation

    MRC Laboratory of Molecular Biology, Cambridge, UK.

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BACTERIORHODOPSINA248Halobacterium salinarumMutation(s): 0 
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Explore P02945 
Go to UniProtKB:  P02945
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
Query on DPG

Download CCD File 
C46 H96 O11 P2
 Ligand Interaction
Query on RET

Download CCD File 
C20 H28 O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
Query on PCA
Experimental Data & Validation

Experimental Data

  • Resolution: 3.50 Å
  • R-Value Work: 0.280 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.45α = 90
b = 62.45β = 90
c = 100.9γ = 120
Software Package:
Software NamePurpose
PICKYCORdata reduction
ANdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-06-10
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2012-05-30
    Changes: Experimental preparation