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PDBsum entry 2g87
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protein ligands metals Protein-protein interface(s) links
Signaling protein PDB id
2g87

 

 

 

 

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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:
2g87
Name: Signaling protein
Title: Crystallographic model of bathorhodopsin
Structure: Rhodopsin. Chain: a, b. Synonym: bathorhodopsin
Source: Bos taurus. Cattle. Organism_taxid: 9913
Biol. unit: Dimer (from PQS)
Resolution:
2.60Å     R-factor:   0.178     R-free:   0.181
Authors: H.Nakamichi,T.Okada
Key ref: H.Nakamichi and T.Okada (2006). Crystallographic analysis of primary visual photochemistry. Angew Chem Int Ed Engl, 45, 4270-4273. PubMed id: 16586416
Date:
02-Mar-06     Release date:   02-Sep-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

 

 
Angew Chem Int Ed Engl 45:4270-4273 (2006)
PubMed id: 16586416  
 
 
Crystallographic analysis of primary visual photochemistry.
H.Nakamichi, T.Okada.
 
  ABSTRACT  
 
No abstract given.

 

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
21240439 P.Garcia-Fernandez, Y.Liu, I.B.Bersuker, and J.E.Boggs (2011).
Pseudo Jahn-Teller origin of cis-trans and other conformational changes. The role of double bonds.
  Phys Chem Chem Phys, 13, 3502-3513.  
  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.  
20042594 T.Matsuyama, T.Yamashita, H.Imai, and Y.Shichida (2010).
Covalent bond between ligand and receptor required for efficient activation in rhodopsin.
  J Biol Chem, 285, 8114-8121.  
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.  
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.  
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.  
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.  
19192210 S.Sekharan (2009).
Water-mediated Spectral Shifts in Rhodopsin and Bathorhodopsin.
  Photochem Photobiol, 85, 517-520.  
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.  
19805066 T.Tada, A.Altun, and S.Yokoyama (2009).
Evolutionary replacement of UV vision by violet vision in fish.
  Proc Natl Acad Sci U S A, 106, 17457-17462.  
18979030 D.Wang, Q.Chen, and L.J.Wan (2008).
Structural transition of molecular assembly under photo-irradiation: an STM study.
  Phys Chem Chem Phys, 10, 6467-6478.  
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.  
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.  
18351404 R.Send, and D.Sundholm (2008).
The molecular structure of a curl-shaped retinal isomer.
  J Mol Model, 14, 717-726.  
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.  
17449675 H.Nakamichi, V.Buss, and T.Okada (2007).
Photoisomerization mechanism of rhodopsin and 9-cis-rhodopsin revealed by x-ray crystallography.
  Biophys J, 92, L106-L108.
PDB code: 2ped
17289671 K.D.Ridge, and K.Palczewski (2007).
Visual rhodopsin sees the light: structure and mechanism of G protein signaling.
  J Biol Chem, 282, 9297-9301.  
18028218 L.Y.Yang, and R.S.Liu (2007).
Mechanism of photoisomerization of 1-naphthyl-2-phenylethylenes in organic glasses.
  Photochem Photobiol, 83, 1436-1440.  
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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