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PDBsum entry 2z73
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Membrane protein PDB id
2z73

 

 

 

 

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Contents
Protein chains
350 a.a. *
Ligands
BOG ×2
RET ×2
PLM ×4
TWT ×2
SO4
PC1
Waters ×57
* Residue conservation analysis
PDB id:
2z73
Name: Membrane protein
Title: Crystal structure of squid rhodopsin
Structure: Rhodopsin. Chain: a, b
Source: Todarodes pacificus. Japanese flying squid
Resolution:
2.50Å     R-factor:   0.188     R-free:   0.206
Authors: M.Murakami,T.Kouyama
Key ref:
M.Murakami and T.Kouyama (2008). Crystal structure of squid rhodopsin. Nature, 453, 363-367. PubMed id: 18480818 DOI: 10.1038/nature06925
Date:
13-Aug-07     Release date:   13-May-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P31356  (OPSD_TODPA) -  Rhodopsin from Todarodes pacificus
Seq:
Struc: 		448 a.a.
350 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1038/nature06925 Nature 453:363-367 (2008)
PubMed id: 18480818  
 
 
Crystal structure of squid rhodopsin.
M.Murakami, T.Kouyama.
 
  ABSTRACT  
 
Invertebrate phototransduction uses an inositol-1,4,5-trisphosphate signalling cascade in which photoactivated rhodopsin stimulates a G(q)-type G protein, that is, a class of G protein that stimulates membrane-bound phospholipase Cbeta. The same cascade is used by many G-protein-coupled receptors, indicating that invertebrate rhodopsin is a prototypical member. Here we report the crystal structure of squid (Todarodes pacificus) rhodopsin at 2.5 A resolution. Among seven transmembrane alpha-helices, helices V and VI extend into the cytoplasmic medium and, together with two cytoplasmic helices, they form a rigid protrusion from the membrane surface. This peculiar structure, which is not seen in bovine rhodopsin, seems to be crucial for the recognition of G(q)-type G proteins. The retinal Schiff base forms a hydrogen bond to Asn 87 or Tyr 111; it is far from the putative counterion Glu 180. In the crystal, a tight association is formed between the amino-terminal polypeptides of neighbouring monomers; this intermembrane dimerization may be responsible for the organization of hexagonally packed microvillar membranes in the photoreceptor rhabdom.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Schematic diagram of the topology of squid rhodopsin. -Helices are denoted by black rectangles, 3[10] helices as grey rectangles and -strands as open arrows. In the current structural model, the polypeptide chain is traced from Glu 9 to Glu 358 (shown by black letters). Grey letters indicate residues that are truncated or disordered. Retinal bound to Lys 305 and palmitoyl bound to Cys 337 are included in the structural model. A disulphide bond is formed between Cys 108 and Cys 186. The counterion Glu 180, residues within 3.5 Å of the Schiff base and within 4 Å of the retinal polyene chain are circled by red, purple and green lines, respectively. Positively and negatively ionizable residues are marked with blue and pink circles, respectively. 		Figure 3.
Figure 3: Structural comparisons between squid rhodopsin and bovine rhodopsin. Squid rhodopsin is denoted by brown and magenta; bovine rhodopsin by cyan and blue.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2008, 453, 363-367) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23407534 A.J.Venkatakrishnan, X.Deupi, G.Lebon, C.G.Tate, G.F.Schertler, and M.M.Babu (2013).
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G-protein-coupled receptor inactivation by an allosteric inverse-agonist antibody.
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PDB codes: 3vg9 3vga
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PDB code: 3rze
20672377 V.Pabuwal, and Z.Li (2011).
Comparison analysis of primary ligand-binding sites in seven-helix membrane proteins.
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20880955 A.Wuster, A.J.Venkatakrishnan, G.F.Schertler, and M.M.Babu (2010).
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Diversity and functional properties of bistable pigments.
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A pivot between helices V and VI near the retinal-binding site is necessary for activation in rhodopsins.
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  PLoS One, 5, e12394.  
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G-protein-coupled receptor structure: what can we learn?
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Comparative sequence and structural analyses of G-protein-coupled receptor crystal structures and implications for molecular models.
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Topology of class A G protein-coupled receptors: insights gained from crystal structures of rhodopsins, adrenergic and adenosine receptors.
  Mol Pharmacol, 75, 1.  
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Chemokine receptors and other G protein-coupled receptors.
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19192200 D.T.Lodowski, T.E.Angel, and K.Palczewski (2009).
Comparative Analysis of GPCR Crystal Structures.
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Dynamics of the internal water molecules in squid rhodopsin.
  Biophys J, 96, 2572-2576.  
19126545 E.Salcedo, D.M.Farrell, L.Zheng, M.Phistry, E.E.Bagg, and S.G.Britt (2009).
The green-absorbing Drosophila Rh6 visual pigment contains a blue-shifting amino acid substitution that is conserved in vertebrates.
  J Biol Chem, 284, 5717-5722.  
19152328 G.K.Umanah, C.Son, F.Ding, F.Naider, and J.M.Becker (2009).
Cross-linking of a DOPA-containing peptide ligand into its G protein-coupled receptor.
  Biochemistry, 48, 2033-2044.  
18828176 G.Skretas, and G.Georgiou (2009).
Genetic analysis of G protein-coupled receptor expression in Escherichia coli: inhibitory role of DnaJ on the membrane integration of the human central cannabinoid receptor.
  Biotechnol Bioeng, 102, 357-367.  
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Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.
  PLoS ONE, 4, e4345.  
19497849 H.Tsukamoto, D.L.Farrens, M.Koyanagi, and A.Terakita (2009).
The magnitude of the light-induced conformational change in different rhodopsins correlates with their ability to activate G proteins.
  J Biol Chem, 284, 20676-20683.  
19276075 I.Domazet, B.J.Holleran, S.S.Martin, P.Lavigne, R.Leduc, E.Escher, and G.Guillemette (2009).
The Second Transmembrane Domain of the Human Type 1 Angiotensin II Receptor Participates in the Formation of the Ligand Binding Pocket and Undergoes Integral Pivoting Movement during the Process of Receptor Activation.
  J Biol Chem, 284, 11922-11929.  
19773549 I.Domazet, S.S.Martin, B.J.Holleran, M.E.Morin, P.Lacasse, P.Lavigne, E.Escher, R.Leduc, and G.Guillemette (2009).
The fifth transmembrane domain of angiotensin II Type 1 receptor participates in the formation of the ligand-binding pocket and undergoes a counterclockwise rotation upon receptor activation.
  J Biol Chem, 284, 31953-31961.  
19572012 I.Kock, N.A.Bulgakova, E.Knust, I.Sinning, and V.Panneels (2009).
Targeting of Drosophila rhodopsin requires helix 8 but not the distal C-terminus.
  PLoS One, 4, e6101.  
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.  
19274719 K.H.Ahn, M.Pellegrini, N.Tsomaia, A.K.Yatawara, D.A.Kendall, and D.F.Mierke (2009).
Structural analysis of the human cannabinoid receptor one carboxyl-terminus identifies two amphipathic helices.
  Biopolymers, 91, 565-573.  
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.  
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Phototransduction motifs and variations.
  Cell, 139, 246-264.  
19141277 M.A.Hanson, and R.C.Stevens (2009).
Discovery of new GPCR biology: one receptor structure at a time.
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Activation induces structural changes in the liganded angiotensin II type 1 receptor.
  J Biol Chem, 284, 26603-26612.  
19166508 R.J.Ward, L.Jenkins, and G.Milligan (2009).
Selectivity and functional consequences of interactions of family A G protein-coupled receptors with neurochondrin and periplakin.
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Ligand binding and micro-switches in 7TM receptor structures.
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Ribosomal S6 kinase 2 directly phosphorylates the 5-hydroxytryptamine 2A (5-HT2A) serotonin receptor, thereby modulating 5-HT2A signaling.
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Rhodopsin and the others: a historical perspective on structural studies of G protein-coupled receptors.
  Curr Pharm Des, 15, 3994-4002.  
19458709 S.H.White (2009).
Biophysical dissection of membrane proteins.
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Expression, purification and in vitro functional reconstitution of the chemokine receptor CCR1.
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Structural waters define a functional channel mediating activation of the GPCR, rhodopsin.
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Crystal structure of opsin in its G-protein-interacting conformation.
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PDB code: 3dqb
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The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist.
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PDB code: 3eml
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Structural insights into G-protein-coupled receptor activation.
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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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