PDBsum entry: 1at9

Photoreceptor

PDB-id: 1at9

Asymmetric unit

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PROCHECK

Protein chain

230 a.a. *

Ligands

RET

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit*, trimer
(*as deduced by PQS)

PDB id:

1at9

Name:

Photoreceptor

Title:

Structure of bacteriorhodopsin at 3.0 angstrom determined by electron crystallography

Structure:

Bacteriorhodopsin. Chain: a

Source:

Halobacterium salinarum. Organism_taxid: 2242. Strain: jw5

Biological unit:

Trimer (from PQS)

UniProt:

P02945 (BACR_HALSA)

Seq:

262 a.a.

Struc:

230 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Resolution:

3.00Å

Authors:

Y.Kimura,D.G.Vassylyev,A.Miyazawa,A.Kidera,M.Matsushima, K.Mitsuoka,K.Murata,T.Hirai,Y.Fujiyoshi

Key ref:

Y.Kimura et al. (1997). Surface of bacteriorhodopsin revealed by high-resolution electron crystallography.. Nature, 389, 206-211. [PubMed id: 9296502] [DOI: 10.1038/38323]

Date:

20-Aug-97

Release date:

16-Sep-98

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Clefts

Surface

Key reference

DOI no: 10.1038/38323

Nature 389:206-211 (1997)

PubMed id: 9296502

Surface of bacteriorhodopsin revealed by high-resolution electron crystallography.

Y.Kimura, D.G.Vassylyev, A.Miyazawa, A.Kidera, M.Matsushima, K.Mitsuoka, K.Murata, T.Hirai, Y.Fujiyoshi.

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. 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.

Selected figure(s)

Figure 3.
Figure 3 Charge distribution in bacteriorhodopsin. The circles represent negative (red) and positive (blue) charges. Asp 96 and Asp 85 are green to show the donor/acceptor of the proton to/from the Schiff base, which connects retinal and Lys 216. Retinal and Lys 216 are shown in purple. a, Charge distribution on the cytoplasmic side of the membrane (input of the proton pump). Asp 96 is surrounded by Asp 36, Asp 38, Asp 102 and Asp 104. This negatively charged cluster is encircled by positively charged protein residues, which are in turn surrounded by negatively charged lipids. b, Charge distribution on the extracellular side of the membrane (output of the proton pump). c, Solid surface view of the cytoplasmic side of bacteriorhodopsin with a potential calculation (viewed as indicated in a). Blue indicates positive and red negative potential. The thin red line is the z-axis. The putative proton entrance is in the vicinity of this line. d, Solid surface view of the extracellular side of bacteriorhodopsin (corresponding to b).

Figure 4.
Figure 4 Possible proton pathway in bacteriorhdopsin. The aspartic acids are located in a plane at the hydrophobic-hydrophilic interface on the cytoplasmic side of the membrane. In contrast, the side chains of Glu 204, Glu 194, Glu 74 and Glu 9 on the extracellular side are aligned along the direction perpendicular to the membrane surface. This view corresponds to that of Fig. 1a, except for the part of the ribbon model of C helix, which was replaced with a yellow coil for visualization.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (1997, 389, 206-211) copyright 1997.

Figures were selected by an automated process.