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Signaling protein PDB id
1u19
Jmol
Contents
Protein chains
349 a.a. *
Ligands
MAN-NAG-NAG
NAG-NAG ×2
RET ×2
PLM ×6
HTG ×4
BMA-BMA-NAG-NAG
HTO
Metals
_HG ×6
_ZN ×7
Waters ×66
* Residue conservation analysis
PDB id:
1u19
Name: Signaling protein
Title: Crystal structure of bovine rhodopsin at 2.2 angstroms resol
Structure: Rhodopsin. Chain: a, b
Source: Bos taurus. Cattle. Organism_taxid: 9913
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.200     R-free:   0.222
Authors: T.Okada,M.Sugihara,A.N.Bondar,M.Elstner,P.Entel,V.Buss
Key ref:
T.Okada et al. (2004). The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure. J Mol Biol, 342, 571-583. PubMed id: 15327956 DOI: 10.1016/j.jmb.2004.07.044
Date:
15-Jul-04     Release date:   12-Oct-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P02699  (OPSD_BOVIN) -  Rhodopsin
Seq:
Struc: 		348 a.a.
348 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     photoreceptor inner segment   8 terms 
  Biological process     response to stimulus   12 terms 
  Biochemical function     signal transducer activity     6 terms  

 

 
DOI no: 10.1016/j.jmb.2004.07.044 J Mol Biol 342:571-583 (2004)
PubMed id: 15327956  
 
 
The retinal conformation and its environment in rhodopsin in light of a new 2.2 A crystal structure.
T.Okada, M.Sugihara, A.N.Bondar, M.Elstner, P.Entel, V.Buss.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal structure model of bovine rhodopsin at 2.2 Å. The two Figures shown are related by a 90° rotation along the vertical axis. Water molecules that are found inside the protein consistently in the two molecules of an asymmetric unit are indicated by light blue spheres. In the right Figure, two heptylthioglucoside molecules are also shown to indicate the approximate range of the transmembrane domain. 		Figure 2.
Figure 2. Retinal chromophore and its environment in the crystal. Top, stereo pair of the 11-cis-retinal Schiff base linked to Lys296. Nitrogen and oxygen atoms are colored in blue and red, respectively. The carbon numbers are marked only for the two bonds that are found to be significantly twisted. Bottom, stereo pair of the chromophore-binding site with some nearby amino acid residues having large contact surface with the retinal.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 342, 571-583) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

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PDB code: 3pbl
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Structural Characterization of a Zinc High-affinity Binding Site in Rhodopsin.
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The Green-absorbing Drosophila Rh6 Visual Pigment Contains a Blue-shifting Amino Acid Substitution That Is Conserved in Vertebrates.
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Distinctions between Hydrophobic Helices in Globular Proteins and Transmembrane Segments as Factors in Protein Sorting.
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PDB code: 1xgy
17060607 D.Salom, D.T.Lodowski, R.E.Stenkamp, I.Le Trong, M.Golczak, B.Jastrzebska, T.Harris, J.A.Ballesteros, and K.Palczewski (2006).
Crystal structure of a photoactivated deprotonated intermediate of rhodopsin.
  Proc Natl Acad Sci U S A, 103, 16123-16128.
PDB codes: 2i35 2i36 2i37
16997914 D.Verzijl, L.Pardo, M.van Dijk, Y.K.Gruijthuijsen, A.Jongejan, H.Timmerman, J.Nicholas, M.Schwarz, P.M.Murphy, R.Leurs, and M.J.Smit (2006).
Helix 8 of the viral chemokine receptor ORF74 directs chemokine binding.
  J Biol Chem, 281, 35327-35335.  
16729264 E.L.Mehler, S.A.Hassan, S.Kortagere, and H.Weinstein (2006).
Ab initio computational modeling of loops in G-protein-coupled receptors: lessons from the crystal structure of rhodopsin.
  Proteins, 64, 673-690.  
16905195 F.Boeckler, and P.Gmeiner (2006).
The structural evolution of dopamine D3 receptor ligands: structure-activity relationships and selected neuropharmacological aspects.
  Pharmacol Ther, 112, 281-333.  
17009093 F.Fanelli, and P.G.De Benedetti (2006).
Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling.
  J Comput Aided Mol Des, 20, 449-461.  
16908857 H.Nakamichi, and T.Okada (2006).
Local peptide movement in the photoreaction intermediate of rhodopsin.
  Proc Natl Acad Sci U S A, 103, 12729-12734.
PDB code: 2hpy
16586416 H.Nakamichi, and T.Okada (2006).
Crystallographic analysis of primary visual photochemistry.
  Angew Chem Int Ed Engl, 45, 4270-4273.
PDB code: 2g87
16605265 I.Szundi, J.J.Ruprecht, J.Epps, C.Villa, T.E.Swartz, J.W.Lewis, G.F.Schertler, and D.S.Kliger (2006).
Rhodopsin photointermediates in two-dimensional crystals at physiological temperatures.
  Biochemistry, 45, 4974-4982.  
16634624 J.W.Lewis, I.Szundi, M.A.Kazmi, T.P.Sakmar, and D.S.Kliger (2006).
Proton movement and photointermediate kinetics in rhodopsin mutants.
  Biochemistry, 45, 5430-5439.  
16407225 K.D.Ridge, N.G.Abdulaev, C.Zhang, T.Ngo, D.M.Brabazon, and J.P.Marino (2006).
Conformational changes associated with receptor-stimulated guanine nucleotide exchange in a heterotrimeric G-protein alpha-subunit: NMR analysis of GTPgammaS-bound states.
  J Biol Chem, 281, 7635-7648.  
16756510 K.Palczewski (2006).
G protein-coupled receptor rhodopsin.
  Annu Rev Biochem, 75, 743-767.  
16941510 M.Domínguez, R.Alvarez, M.Pérez, K.Palczewski, and A.R.de Lera (2006).
The role of the 11-cis-retinal ring methyl substituents in visual pigment formation.
  Chembiochem, 7, 1815-1825.  
17089205 M.Filizola, S.X.Wang, and H.Weinstein (2006).
Dynamic models of G-protein coupled receptor dimers: indications of asymmetry in the rhodopsin dimer from molecular dynamics simulations in a POPC bilayer.
  J Comput Aided Mol Des, 20, 405-416.  
16333859 M.J.Slusarz, R.Slusarz, and J.Ciarkowski (2006).
Investigation of mechanism of desmopressin binding in vasopressin V2 receptor versus vasopressin V1a and oxytocin receptors: molecular dynamics simulation of the agonist-bound state in the membrane-aqueous system.
  Biopolymers, 81, 321-338.  
16906791 M.R.Lewis, and M.Kono (2006).
Rhodopsin deactivation is affected by mutations of Tyrl91.
  Photochem Photobiol, 82, 1442-1446.  
16729349 M.Schreiber, M.Sugihara, T.Okada, and V.Buss (2006).
Quantum mechanical studies on the crystallographic model of bathorhodopsin.
  Angew Chem Int Ed Engl, 45, 4274-4277.  
17043908 M.Wanko, M.Hoffmann, T.Frauenheim, and M.Elstner (2006).
Computational photochemistry of retinal proteins.
  J Comput Aided Mol Des, 20, 511-518.  
17009091 N.Singh, G.Chevé, D.M.Ferguson, and C.R.McCurdy (2006).
A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist.
  J Comput Aided Mol Des, 20, 471-493.  
16283119 O.Weingart, I.Schapiro, and V.Buss (2006).
Bond torsion affects the product distribution in the photoreaction of retinal model chromophores.
  J Mol Model, 12, 713-721.  
17090682 P.B.Coto, A.Strambi, N.Ferré, and M.Olivucci (2006).
The color of rhodopsins at the ab initio multiconfigurational perturbation theory resolution.
  Proc Natl Acad Sci U S A, 103, 17154-17159.  
  16796383 P.H.Reggio (2006).
Computational methods in drug design: modeling G protein-coupled receptor monomers, dimers, and oligomers.
  AAPS J, 8, E322-E336.  
16972169 S.Kortagere, A.Roy, and E.L.Mehler (2006).
Ab initio computational modeling of long loops in G-protein coupled receptors.
  J Comput Aided Mol Des, 20, 427-436.  
16319069 S.Marion, R.H.Oakley, K.M.Kim, M.G.Caron, and L.S.Barak (2006).
A beta-arrestin binding determinant common to the second intracellular loops of rhodopsin family G protein-coupled receptors.
  J Biol Chem, 281, 2932-2938.  
16343816 S.Yokoyama, W.T.Starmer, Y.Takahashi, and T.Tada (2006).
Tertiary structure and spectral tuning of UV and violet pigments in vertebrates.
  Gene, 365, 95.  
16402913 T.W.Schwartz, T.M.Frimurer, B.Holst, M.M.Rosenkilde, and C.E.Elling (2006).
Molecular mechanism of 7TM receptor activation--a global toggle switch model.
  Annu Rev Pharmacol Toxicol, 46, 481-519.  
16460808 V.V.Gurevich, and E.V.Gurevich (2006).
The structural basis of arrestin-mediated regulation of G-protein-coupled receptors.
  Pharmacol Ther, 110, 465-502.  
17098868 X.Zhao, Y.Nagai, P.J.Reeves, P.Kiley, H.G.Khorana, and S.Zhang (2006).
Designer short peptide surfactants stabilize G protein-coupled receptor bovine rhodopsin.
  Proc Natl Acad Sci U S A, 103, 17707-17712.  
15774036 A.Terakita (2005).
The opsins.
  Genome Biol, 6, 213.  
16247601 B.Schlegel, W.Sippl, and H.D.Höltje (2005).
Molecular dynamics simulations of bovine rhodopsin: influence of protonation states and different membrane-mimicking environments.
  J Mol Model, 12, 49-64.  
15845544 C.Ambrosio, P.Molinari, F.Fanelli, Y.Chuman, M.Sbraccia, O.Ugur, and T.Costa (2005).
Different structural requirements for the constitutive and the agonist-induced activities of the beta2-adrenergic receptor.
  J Biol Chem, 280, 23464-23474.  
15786429 F.Blomgren, and S.Larsson (2005).
Exploring the potential energy surface of retinal, a comparison of the performance of different methods.
  J Comput Chem, 26, 738-742.  
16027155 F.J.Bartl, O.Fritze, E.Ritter, R.Herrmann, V.Kuksa, K.Palczewski, K.P.Hofmann, and O.P.Ernst (2005).
Partial agonism in a G Protein-coupled receptor: role of the retinal ring structure in rhodopsin activation.
  J Biol Chem, 280, 34259-34267.