1AT9

STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 2.8 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

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: 206-211

  • DOI: 10.1038/38323

  • PubMed Abstract: 
  • Bacteriorhodopsin is a transmembrane protein that uses light energy, absorbed by its chromophore retinal, to pump protons from the cytoplasm of bacteria such as Halobacterium salinarium into the extracellular space. It is made up of seven alpha-helic ...

    Bacteriorhodopsin is a transmembrane protein that uses light energy, absorbed by its chromophore retinal, to pump protons from the cytoplasm of bacteria such as Halobacterium salinarium into the extracellular space. It is made up of seven alpha-helices, and in the bacterium forms natural, two-dimensional crystals called purple membranes. We have analysed these crystals by electron cryo-microscopy to obtain images of bacteriorhodopsin at 3.0 A resolution. The structure covers nearly all 248 amino acids, including loops outside the membrane, and reveals the distribution of charged residues on both sides of the membrane surface. In addition, analysis of the electron-potential map produced by this method allows the determination of the charge status of these residues. On the extracellular side, four glutamate residues surround the entrance to the proton channel, whereas on the cytoplasmic side, four aspartic acids occur in a plane at the boundary of the hydrophobic-hydrophilic interface. The negative charges produced by these aspartate residues is encircled by areas of positive charge that may facilitate accumulation and lateral movement of protons on this surface.


    Related Citations: 
    • 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
    • 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


    Organizational Affiliation

    Biomolecular Engineering Research Institute, Osaka, Japan. kimuray@beri.co.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
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Bacterial and Algal Rhodopsins
Protein: 
Bacteriorhodopsin (BR)
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1))
Go to UniProtKB:  P02945
Small Molecules
Ligands 1 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
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: 2.8 Å
  • Aggregation State: 2D ARRAY 
  • Reconstruction Method: CRYSTALLOGRAPHY 
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-09-16
    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