PDBsum entry 1x0s

Proton transport

PDB id: 1x0s

Contents

Protein chain

227 a.a. *

Ligands

GLC-MAN-GAL

SO4

RET

L3P ×4

L2P

Waters ×42

* Residue conservation analysis

PDB id:

1x0s

Name:

Proton transport

Title:

Crystal structure of the 13-cis isomer of bacteriorhodopsin

Structure:

Bacteriorhodopsin. Chain: a. Synonym: br

Source:

Halobacterium salinarum. Organism_taxid: 2242. Strain: jw3

Biol. unit:

Trimer (from PDB file)

Resolution:

2.50Å R-factor: 0.271 R-free: 0.305

Authors:

T.Nishikawa,M.Murakami,T.Kouyama

Key ref:

T.Nishikawa et al. (2005). Crystal structure of the 13-cis isomer of bacteriorhodopsin in the dark-adapted state. J Mol Biol, 352, 319-328. PubMed id: 16084526 DOI: 10.1016/j.jmb.2005.07.021

Date:

28-Mar-05 Release date: 30-Aug-05

Protein chain

P02945  (BACR_HALSA) -  Bacteriorhodopsin from Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)

Seq: 262 a.a.

Struc: 227 a.a.

DOI no: 10.1016/j.jmb.2005.07.021

J Mol Biol 352:319-328 (2005)

PubMed id: 16084526

Crystal structure of the 13-cis isomer of bacteriorhodopsin in the dark-adapted state.

T.Nishikawa, M.Murakami, T.Kouyama.

ABSTRACT

The atomic structure of the trans isomer of bacteriorhodopsin was determined previously by using a 3D crystal belonging to the space group P622. Here, a structure is reported for another isomer with the 13-cis, 15-syn retinal in a dark-adapted crystal. Structural comparison of the two isomers indicates that retinal isomerization around the C13[double bond]C14 and the C15[double bond]N bonds is accompanied by noticeable displacements of a few residues in the vicinity of the retinal Schiff base and small re-arrangement of the hydrogen-bonding network in the proton release channel. On the other hand, aromatic residues surrounding the retinal polyene chain were found to scarcely move during the dark/light adaptation. This result suggests that variation in the structural rigidity within the retinal-binding pocket is one of the important factors ensuring the stereospecific isomerization of retinal.

Selected figure(s)

Figure 2.
Figure 2. F[0]−F[0] difference map (|F[DA]|−|F[LA]|) between the dark-adapted and the light-adapted states, contoured at 3.6 σ (positive in yellow and negative in purple) and overlaid on the structure model of the 13-cis isomer. The retinal-Lys216 chain and a sulfate ion are drawn in red; the glycolipids located in the central part of the trimeric structure are in gray. Figure 2. F[0]−F[0] difference map (|F[DA]|−|F[LA]|) between the dark-adapted and the light-adapted states, contoured at 3.6 σ (positive in yellow and negative in purple) and overlaid on the structure model of the 13-cis isomer. The retinal-Lys216 chain and a sulfate ion are drawn in red; the glycolipids located in the central part of the trimeric structure are in gray. This Figure and [3]Figure 3, [4]Figure 4, [5]Figure 5 and [6]Figure 7 are drawn with XtalView.[7]^49

Figure 7.
Figure 7. Structural comparison between the 13-cis isomer (gold, blue and red), the all-trans isomer (cyan) and the L intermediate (yellow). Figure 7. Structural comparison between the 13-cis isomer (gold, blue and red), the all-trans isomer (cyan) and the L intermediate (yellow).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 352, 319-328) copyright 2005.

Figures were selected by an automated process.