2AT9

STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM BY ELECTRON CRYSTALLOGRAPHY


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: CRYSTALLOGRAPHY 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of bacteriorhodopsin at 3.0 A resolution based on electron crystallography: implication of the charge distribution.

Mitsuoka, K.Hirai, T.Murata, K.Miyazawa, A.Kidera, A.Kimura, Y.Fujiyoshi, Y.

(1999) J.Mol.Biol. 286: 861-882

  • DOI: 10.1006/jmbi.1998.2529

  • PubMed Abstract: 
  • Electron crystallography has the potential to visualise the charge status of atoms. This is due to the significantly different scattering factors of neutral and ionised atoms for electrons in the low-resolution range (typically less than 5 A). In pre ...

    Electron crystallography has the potential to visualise the charge status of atoms. This is due to the significantly different scattering factors of neutral and ionised atoms for electrons in the low-resolution range (typically less than 5 A). In previous work, we observed two different types of densities around acidic residues in the experimental (|Fo|) map of bacteriorhodopsin (bR), a light-driven proton pump. We suggested that these might reflect different states of the acidic residues; namely, the protonated (neutral) and the deprotonated (negatively charged) state. To evaluate the observed charge more quantitatively, we refined the atomic model for bR and eight surrounding lipids using our electron crystallographic data set between 8.0 and 3.0 A resolution, where the charge effect is small. The refined model yielded an R-factor of 23.7% and a free R-factor of 33.0%. To evaluate the effect of charges on the density map, we calculated a difference (|Fo|-|Fc|) map including data of a resolution lower than 8.0 A resolution, where the charge effect is significant. We found strong peaks in the difference map mainly in the backbone region of the transmembrane helices. We interpreted these peaks to come from the polarisation of the polar groups in the main chain of the alpha-helices and we examined this by assuming a partial charge of 0.5 for the peptide carbonyl groups. The resulting R and free R-factors dropped from 0.250 and 0.341 to 0.246 and 0.336, respectively. Furthermore, we also observed some strong peaks around some side-chains, which could be assigned to positively charged atoms. Thus, we could show that Asp36 and Asp102 are likely to interact with cations nearby. In addition, peaks found around the acidic residues Glu74, Glu194 and Glu212 have different features and might represent positive charges on polarised water molecules or hydroxonium ions.


    Related Citations: 
    • 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
    • Proton Transfer Pathways in Bacteriorhodopsin at 2.3 Angstrom Resolution
      Luecke, H.,Richter, H.T.,Lanyi, J.K.
      (1998) Science 280: 1934
    • Surface of Bacteriorhodopsin Revealed by High-Resolution Electron Crystallography
      Kimura, Y.,Vassylyev, D.G.,Miyazawa, A.,Kidera, A.,Matsushima, M.,Mitsuoka, K.,Murata, K.,Hirai, T.,Fujiyoshi, Y.
      (1997) Nature 389: 206
    • 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


    Organizational Affiliation

    Department of Biophysics Faculty of Science, Kyoto University, Oiwake-cho Kitashirakawa, Sakyo-ku, Kyoto, 606-8502, Japan. kaorum@em.biophys.kyoto-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BACTERIORHODOPSIN
A
248Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)Gene Names: bop
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Go to UniProtKB:  P02945
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download SDF File 
Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
2DP
Query on 2DP

Download SDF File 
Download CCD File 
A
3-[[3-METHYLPHOSPHONO-GLYCEROLYL]PHOSPHONYL]-[1,2-DI[2,6,10,14-TETRAMETHYL-HEXADECAN-16-YL]GLYCEROL
C47 H98 O11 P2
ORVRQEXCVQTLMU-JCHKDBOHSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
A
L-PEPTIDE LINKINGC5 H7 N O3GLU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: CRYSTALLOGRAPHY 
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance