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PDBsum entry 2hpy
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protein ligands metals Protein-protein interface(s) links
Signaling protein PDB id
2hpy

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
349 a.a. *
Ligands
NAG-NAG-MAN
NAG-NAG ×2
NAG-NAG-BMA-BMA
RET ×2
PLM ×6
HTG ×4
HTO
Metals
_HG ×6
_ZN ×7
Waters ×66
* Residue conservation analysis
PDB id:
2hpy
Name: Signaling protein
Title: Crystallographic model of lumirhodopsin
Structure: Rhodopsin. Chain: a, b
Source: Bos taurus. Cattle. Organism_taxid: 9913
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.218     R-free:   0.238
Authors: H.Nakamichi,T.Okada
Key ref:
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. PubMed id: 16908857 DOI: 10.1073/pnas.0601765103
Date:
18-Jul-06     Release date:   22-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 

 
DOI no: 10.1073/pnas.0601765103 Proc Natl Acad Sci U S A 103:12729-12734 (2006)
PubMed id: 16908857  
 
 
Local peptide movement in the photoreaction intermediate of rhodopsin.
H.Nakamichi, T.Okada.
 
  ABSTRACT  
 
Photoactivation of the visual rhodopsin, a prototypical G protein-coupled receptor (GPCR), involves efficient conversion of the intrinsic inverse-agonist 11-cis-retinal to the all-trans agonist. This event leads to the rearrangement of the heptahelical transmembrane bundle, which is thought to be shared by hundreds of GPCRs. To examine this activation mechanism, we determined the x-ray crystallographic model of the photoreaction intermediate of rhodopsin, lumirhodopsin, which represents the conformational state having the nearly complete all-trans agonist form of the retinal. A difference electron density map clearly indicated that the distorted all-trans-retinal in the precedent intermediate bathorhodopsin relaxes by dislocation of the beta-ionone ring in lumirhodopsin, along with significant peptide displacement in the middle of helix III, including approximately two helical turns. This local movement results in the breaking of the electrostatic interhelical restraints mediated by many of the conserved residues among rhodopsin-like GPCRs, with consequent acquisition of full activity.
 
  Selected figure(s)  
 
Figure 3.
Fig. 3. Differences between RHO and LUMI. (A–C) Projection views of the three regions containing the difference electron densities between RHO and LUMI. Each image is a 10-Šslab section from the extracellular (A) to cytoplasmic (C) side of the transmembrane helical domain. Positive (blue) and negative (red) electron densities contoured to 3.5 level are shown on the -carbon traces of the seven helices. (D) Superposition of the crystallographic models of RHO (green) and LUMI (orange). Only the -carbon traces and the retinal chromophore are shown. 		Figure 4.
Fig. 4. Crystallographic models of the three states of RHO. (A) Projection view around the retinal with some amino acid residues. Shown are the three models: RHO (green), BATHO (red), and LUMI (orange). (B) Structural changes between RHO (green) and LUMI (orange) around the middle of helix III. The four bound water molecules in this site are shown as small light blue spheres, which are fixed in the positions found in the ground-state structure.
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20708633 H.W.Choe, J.H.Park, Y.J.Kim, and O.P.Ernst (2011).
Transmembrane signaling by GPCRs: insight from rhodopsin and opsin structures.
  Neuropharmacology, 60, 52-57.  
21389988 H.W.Choe, Y.J.Kim, J.H.Park, T.Morizumi, E.F.Pai, N.Krauss, K.P.Hofmann, P.Scheerer, and O.P.Ernst (2011).
Crystal structure of metarhodopsin II.
  Nature, 471, 651-655.
PDB codes: 3pqr 3pxo
21389983 J.Standfuss, P.C.Edwards, A.D'Antona, M.Fransen, G.Xie, D.D.Oprian, and G.F.Schertler (2011).
The structural basis of agonist-induced activation in constitutively active rhodopsin.
  Nature, 471, 656-660.
PDB code: 2x72
20423327 B.Jastrzebska, Y.Tsybovsky, and K.Palczewski (2010).
Complexes between photoactivated rhodopsin and transducin: progress and questions.
  Biochem J, 428, 1.  
20483344 D.Provasi, and M.Filizola (2010).
Putative active states of a prototypic g-protein-coupled receptor from biased molecular dynamics.
  Biophys J, 98, 2347-2355.  
20230054 E.Zaitseva, M.F.Brown, and R.Vogel (2010).
Sequential rearrangement of interhelical networks upon rhodopsin activation in membranes: the Meta II(a) conformational substate.
  J Am Chem Soc, 132, 4815-4821.  
20053991 H.Tsukamoto, A.Terakita, and Y.Shichida (2010).
A pivot between helices V and VI near the retinal-binding site is necessary for activation in rhodopsins.
  J Biol Chem, 285, 7351-7357.  
19785456 I.Bahar, T.R.Lezon, A.Bakan, and I.H.Shrivastava (2010).
Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.
  Chem Rev, 110, 1463-1497.  
  20633362 J.A.Goncalves, S.Ahuja, S.Erfani, M.Eilers, and S.O.Smith (2010).
Structure and function of G protein-coupled receptors using NMR spectroscopy.
  Prog Nucl Magn Reson Spectrosc, 57, 159-180.  
20886156 K.Sakai, Y.Imamoto, T.Yamashita, and Y.Shichida (2010).
Functional analysis of the second extracellular loop of rhodopsin by characterizing split variants.
  Photochem Photobiol Sci, 9, 1490-1497.  
20192770 S.O.Smith (2010).
Structure and activation of the visual pigment rhodopsin.
  Annu Rev Biophys, 39, 309-328.  
20004206 V.Hornak, S.Ahuja, M.Eilers, J.A.Goncalves, M.Sheves, P.J.Reeves, and S.O.Smith (2010).
Light activation of rhodopsin: insights from molecular dynamics simulations guided by solid-state NMR distance restraints.
  J Mol Biol, 396, 510-527.  
20940434 X.Deupi, and B.K.Kobilka (2010).
Energy landscapes as a tool to integrate GPCR structure, dynamics, and function.
  Physiology (Bethesda), 25, 293-303.  
18945819 D.Mustafi, and K.Palczewski (2009).
Topology of class A G protein-coupled receptors: insights gained from crystal structures of rhodopsins, adrenergic and adenosine receptors.
  Mol Pharmacol, 75, 1.  
19192200 D.T.Lodowski, T.E.Angel, and K.Palczewski (2009).
Comparative Analysis of GPCR Crystal Structures.
  Photochem Photobiol, 85, 425-430.  
19627087 J.C.Mobarec, R.Sanchez, and M.Filizola (2009).
Modern homology modeling of G-protein coupled receptors: which structural template to use?
  J Med Chem, 52, 5207-5216.  
19357801 J.Devillé, J.Rey, and M.Chabbert (2009).
An indel in transmembrane helix 2 helps to trace the molecular evolution of class A G-protein-coupled receptors.
  J Mol Evol, 68, 475-489.  
19836958 K.P.Hofmann, P.Scheerer, P.W.Hildebrand, H.W.Choe, J.H.Park, M.Heck, and O.P.Ernst (2009).
A G protein-coupled receptor at work: the rhodopsin model.
  Trends Biochem Sci, 34, 540-552.  
18692154 M.B.Morris, S.Dastmalchi, and W.B.Church (2009).
Rhodopsin: structure, signal transduction and oligomerisation.
  Int J Biochem Cell Biol, 41, 721-724.  
19267870 M.F.Brown, K.Martínez-Mayorga, K.Nakanishi, G.F.Salgado, and A.V.Struts (2009).
Retinal Conformation and Dynamics in Activation of Rhodopsin Illuminated by Solid-state H NMR Spectroscopy.
  Photochem Photobiol, 85, 442-453.  
19176531 S.Ahuja, E.Crocker, M.Eilers, V.Hornak, A.Hirshfeld, M.Ziliox, N.Syrett, P.J.Reeves, H.G.Khorana, M.Sheves, and S.O.Smith (2009).
Location of the retinal chromophore in the activated state of rhodopsin*.
  J Biol Chem, 284, 10190-10201.  
20028316 S.Costanzi, J.Siegel, I.G.Tikhonova, and K.A.Jacobson (2009).
Rhodopsin and the others: a historical perspective on structural studies of G protein-coupled receptors.
  Curr Pharm Des, 15, 3994-4002.  
19706523 T.E.Angel, S.Gupta, B.Jastrzebska, K.Palczewski, and M.R.Chance (2009).
Structural waters define a functional channel mediating activation of the GPCR, rhodopsin.
  Proc Natl Acad Sci U S A, 106, 14367-14372.  
18501204 A.L.Parrill (2008).
Lysophospholipid interactions with protein targets.
  Biochim Biophys Acta, 1781, 540-546.  
18422873 E.Ritter, M.Elgeti, and F.J.Bartl (2008).
Activity switches of rhodopsin.
  Photochem Photobiol, 84, 911-920.  
18620390 I.G.Tikhonova, R.B.Best, S.Engel, M.C.Gershengorn, G.Hummer, and S.Costanzi (2008).
Atomistic insights into rhodopsin activation from a dynamic model.
  J Am Chem Soc, 130, 10141-10149.  
19672320 J.C.Mobarec, and M.Filizola (2008).
Advances in the Development and Application of Computational Methodologies for Structural Modeling of G-Protein Coupled Receptors.
  Expert Opin Drug Discov, 3, 343-355.  
18563085 J.H.Park, P.Scheerer, K.P.Hofmann, H.W.Choe, and O.P.Ernst (2008).
Crystal structure of the ligand-free G-protein-coupled receptor opsin.
  Nature, 454, 183-187.
PDB code: 3cap
18511075 J.Standfuss, E.Zaitseva, M.Mahalingam, and R.Vogel (2008).
Structural impact of the E113Q counterion mutation on the activation and deactivation pathways of the G protein-coupled receptor rhodopsin.
  J Mol Biol, 380, 145-157.  
17848137 P.S.Park, D.T.Lodowski, and K.Palczewski (2008).
Activation of g protein-coupled receptors: beyond two-state models and tertiary conformational changes.
  Annu Rev Pharmacol Toxicol, 48, 107-141.  
18818650 P.Scheerer, J.H.Park, P.W.Hildebrand, Y.J.Kim, N.Krauss, H.W.Choe, K.P.Hofmann, and O.P.Ernst (2008).
Crystal structure of opsin in its G-protein-interacting conformation.
  Nature, 455, 497-502.
PDB code: 3dqb
  18590333 S.C.Schürer, S.J.Brown, P.J.Gonzalez-Cabrera, M.T.Schaeffer, J.Chapman, E.Jo, P.Chase, T.Spicer, P.Hodder, and H.Rosen (2008).
Ligand-binding pocket shape differences between sphingosine 1-phosphate (S1P) receptors S1P1 and S1P3 determine efficiency of chemical probe identification by ultrahigh-throughput screening.
  ACS Chem Biol, 3, 486-498.  
18759470 V.Subramaniam, G.D.D'Ambruoso, H.K.Hall, R.J.Wysocki, M.F.Brown, and S.S.Saavedra (2008).
Reconstitution of rhodopsin into polymerizable planar supported lipid bilayers: influence of dienoyl monomer structure on photoactivation.
  Langmuir, 24, 11067-11075.  
18399920 Y.Imamoto, and Y.Shichida (2008).
Thermal recovery of iodopsin from photobleaching intermediates.
  Photochem Photobiol, 84, 941-948.  
18346085 Y.Wang, P.H.Bovee-Geurts, J.Lugtenburg, and W.J.DeGrip (2008).
Alpha-retinals as rhodopsin chromophores--preference for the 9-Z configuration and partial agonist activity.
  Photochem Photobiol, 84, 889-894.  
17173267 L.Pardo, X.Deupi, N.Dölker, M.L.López-Rodríguez, and M.Campillo (2007).
The role of internal water molecules in the structure and function of the rhodopsin family of G protein-coupled receptors.
  Chembiochem, 8, 19-24.  
17959373 T.De la Mora-Rey, and C.M.Wilmot (2007).
Synergy within structural biology of single crystal optical spectroscopy and X-ray crystallography.
  Curr Opin Struct Biol, 17, 580-586.  
17502106 Y.Kong, and M.Karplus (2007).
The signaling pathway of rhodopsin.
  Structure, 15, 611-623.  
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
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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