2ZIY

Crystal structure of squid rhodopsin

Summary for 2ZIY

DescriptorRhodopsin, RETINAL, PALMITIC ACID (3 entities in total)
Functional Keywordstransmembrane helices, chromophore, g-protein coupled receptor, glycoprotein, lipoprotein, palmitate, phosphoprotein, photoreceptor protein, receptor, retinal protein, sensory transduction, transducer, vision, signaling protein
Biological sourceTodarodes pacificus (Japanese flying squid)
Cellular locationMembrane; Multi-pass membrane protein P31356
Total number of polymer chains1
Total molecular weight42626.03
Authors
Miyano, M.,Shimamura, T. (deposition date: 2008-02-27, release date: 2008-05-06, Last modification date: 2011-07-13)
Primary citation
Shimamura, T.,Hiraki, K.,Takahashi, N.,Hori, T.,Ago, H.,Masuda, K.,Takio, K.,Ishiguro, M.,Miyano, M.
Crystal structure of squid rhodopsin with intracellularly extended cytoplasmic region
J.Biol.Chem., 283:17753-17756, 2008
PubMed: 18463093 (PDB entries with the same primary citation)
DOI: 10.1074/jbc.C800040200
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3.7 Å)
?

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.352508.4%9.6%5.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 2ziy
no rotation
Molmil generated image of 2ziy
rotated about x axis by 90°
Molmil generated image of 2ziy
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 2ziy
no rotation
Molmil generated image of 2ziy
rotated about x axis by 90°
Molmil generated image of 2ziy
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (2ziy.pdb1.gz [55.03 KB])
Coordinate files for Biological unit (2ziy.pdb2.gz [108.34 KB])
PDBj@FacebookPDBj@TwitterwwPDBwwPDB Foundation

Copyright © 2013-2019 Protein Data Bank Japan