1R84: NMR structure of the 13-cis-15-syn retinal in dark_adapted bacteriorhodopsin

The two forms of bacteriorhodopsin present in the dark-adapted state, containing either all-trans or 13-cis,15-syn retinal, were examined by using solution state NMR, and their structures were determined. Comparison of the all-trans and the 13-cis,15-syn forms shows a shift in position of about 0.25 A within the pocket of the protein. Comparing this to the 13-cis,15-anti chromophore of the catalytic cycle M-intermediate structure, the 13-cis,15-syn form demonstrates a less pronounced up-tilt of the retinal C12[bond]C14 region, while leaving W182 and T178 essentially unchanged. The N[bond]H dipole of the Schiff base orients toward the extracellular side in both forms, however, it reorients toward the intracellular side in the 13-cis,15-anti configuration to form the catalytic M-intermediate. Thus, the change of the N[bond]H dipole is considered primarily responsible for energy storage, conformation changes of the protein, and the deprotonation of the Schiff base. The structural similarity of the all-trans and 13-cis,15-syn forms is taken as strong evidence for the ion dipole dragging model by which proton (hydroxide ion) translocation follows the change of the dipole.
PDB ID: 1R84Download
MMDB ID: 25465
PDB Deposition Date: 2003/10/23
Updated in MMDB: 2003/12
Experimental Method:
solution nmr
Source Organism:
Similar Structures:
Molecular Components in 1R84
Label Count Molecule
Protein (1 molecule)
Bacteriorhodopsin(Gene symbol: VNG_RS05715)
Molecule annotation
Chemical (1 molecule)
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