1AT9

STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM DETERMINED BY ELECTRON CRYSTALLOGRAPHY


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3.00 Å

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
  • Primary Citation of Related Structures:  
    1AT9

  • 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-helices, and in the bacterium forms natural, two-dimensional crystals called purple membranes ...

    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: 
    • 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
    • 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

    Biomolecular Engineering Research Institute, Osaka, Japan. kimuray@beri.co.jp



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BACTERIORHODOPSINA248Halobacterium salinarumMutation(s): 0 
Membrane Entity: Yes 
UniProt
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 (Subject of Investigation/LOI)
Query on RET

Download Ideal Coordinates CCD File 
B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PCA
Query on PCA
AL-PEPTIDE LINKINGC5 H7 N O3GLN
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 3.00 Å
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.45α = 90
b = 62.45β = 90
c = 100γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-09-16
    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