1U19

Crystal Structure of Bovine Rhodopsin at 2.2 Angstroms Resolution

Summary for 1U19

• Entry DOI: 10.2210/pdb1u19/pdb
• Related: 1F88 1HZX 1L9H
• Descriptor: Rhodopsin, HEPTANE-1,2,3-TRIOL, alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ... (11 entities in total)
• Functional Keywords: g protein-coupled receptor, membrane protein, retinal protein, photoreceptor, signaling protein
• Biological source: Bos taurus (cattle)
• Cellular location: Membrane; Multi-pass membrane protein: P02699
• Total number of polymer chains: 2
• Total formula weight: 85393.66

Authors

Okada, T.,Sugihara, M.,Bondar, A.N.,Elstner, M.,Entel, P.,Buss, V. (deposition date: 2004-07-15, release date: 2004-10-12, Last modification date: 2024-10-09)

Primary citation

Okada, T.,Sugihara, M.,Bondar, A.N.,Elstner, M.,Entel, P.,Buss, V.
The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure
J.Mol.Biol., 342:571-583, 2004

PubMed Abstract: A new high-resolution structure is reported for bovine rhodopsin, the visual pigment in rod photoreceptor cells. Substantial improvement of the resolution limit to 2.2 A has been achieved by new crystallization conditions, which also reduce significantly the probability of merohedral twinning in the crystals. The new structure completely resolves the polypeptide chain and provides further details of the chromophore binding site including the configuration about the C6-C7 single bond of the 11-cis-retinal Schiff base. Based on both an earlier structure and the new improved model of the protein, a theoretical study of the chromophore geometry has been carried out using combined quantum mechanics/force field molecular dynamics. The consistency between the experimental and calculated chromophore structures is found to be significantly improved for the 2.2 A model, including the angle of the negatively twisted 6-s-cis-bond. Importantly, the new crystal structure refinement reveals significant negative pre-twist of the C11-C12 double bond and this is also supported by the theoretical calculation although the latter converges to a smaller value. Bond alternation along the unsaturated chain is significant, but weaker in the calculated structure than the one obtained from the X-ray data. Other differences between the experimental and theoretical structures in the chromophore binding site are discussed with respect to the unique spectral properties and excited state reactivity of the chromophore.

PubMed: 15327956
DOI: 10.1016/j.jmb.2004.07.044

Experimental method

X-RAY DIFFRACTION (2.2 Å)