{"id":93,"ordering":636.0,"pdbid":"1gzm","name":"Rhodopsin, inactive, with 11-cis retinal","description":null,"comments":"Structures of intermediate states: bathorhodopsin (2g87) and lumirhodopsin (2hpy). Complex with 9-cis retinal: 2ped.","resolution":"2.65","topology_subunit":"A","topology_show_in":false,"thickness":32.2,"thicknesserror":1.5,"subunit_segments":7,"tilt":11,"tilterror":1,"gibbs":-75.6,"tau":"","verification":"Results are consitent with X-ray scattering  (Blaurock and Wilkins 1972), chemical modification (Barclay and Findlay 1984, Davison and Findlay 1986a,b) and electron microscopy (Krebs et al.  2003) studies. Hydrophobic boundaries of rhodopsin expand when calculated with detergent parameters, in agreement with results of Hubbell et al. (2003).","family_name_cache":"G-protein coupled receptors, family A","species_name_cache":"Bos taurus","membrane_name_cache":"Eykaryo. plasma","membrane_id":4,"species_id":6,"family_id":14,"superfamily_id":6,"classtype_id":1,"type_id":1,"secondary_representations_count":4,"structure_subunits_count":1,"citations_count":6,"uniprotcodes":["OPSD_BOVIN"],"family":{"id":14,"name":"G-protein coupled receptors, family A","pfam":"PF00001","interpro":"IPR000276","tcdb":"9.A.14","primary_structures_count":664,"superfamily":{"id":6,"name":"Rhodopsin-like receptors and pumps","pfam":"CL0192","tcdb":"","families_count":12,"classtype":{"id":1,"name":"Alpha-helical polytopic","superfamilies_count":156,"type":{"id":1,"name":"Transmembrane","classtypes_count":3}}}},"species":{"id":6,"name":"Bos taurus","description":"Eukaryota, Opisthokonta, Metazoa, Eumetazoa, Bilateria, Deuterostomia, Chordata, Craniata, Vertebrata, Gnathostomata (jawed vertebrates), Teleostomi, Euteleostomi, Sarcopterygii, Dipnotetrapodomorpha, Tetrapoda, Amniota, Mammalia, Theria, Eutheria, Boreoeutheria, Laurasiatheria, Artiodactyla, Ruminantia, Pecora, Bovidae, Bovinae, Bos (oxen","primary_structures_count":178},"membrane":{"id":4,"name":"Eukaryotic plasma membrane","primary_structures_count":3316,"short_name":"Eykaryo. plasma","abbrevation":null,"topology_in":"cytoplasmic side","topology_out":"extracellular side","lipid_references":"Ingolfsson, H. I., M. N. Melo, F. J. van Eerden, C. Arnarez, C. A. Lopez, T. A. Wassenaar, X. Periole, A. H. de Vries, D. P. Tieleman and S. J. Marrink (2014). \"Lipid organization of the plasma membrane.\" J Am Chem Soc 136(41): 14554-14559.; Rivel, T., C. Ramseyer and S. Yesylevskyy (2019). \"The asymmetry of plasma membranes and their cholesterol content influence the uptake of cisplatin.\" Sci Rep 9(1): 5627.","lipid_pubmed":"25229711;30948733"},"subunits":[{"ordering":41.0,"name":null,"description":null,"comments":null,"protein_letter":"A","uniprod_id1":null,"uniprod_id2":null,"uniprod_link":null,"tilt":"11","segment":"1(35-63),2(74-99),3(109-133),4(153-172),5(202-224),6(253-276),7(286-308)","assembly_id":5}],"secondary_representations":[{"id":475,"pdbid":"2i35","resolution":"3.8"},{"id":474,"pdbid":"2j4y","resolution":"3.4"},{"id":476,"pdbid":"3c9l","resolution":"2.65"},{"id":477,"pdbid":"3c9m","resolution":"3.4"}],"citations":[{"id":14,"ordering":14.0,"name":"","maintext":"Hubbell WL, Altenbach C, Hubbell CM, and Khorana HG (2003) Rhodopsin structure, dynamics, and activation: A perspective from crystallography, site-directed spin labeling, sulfhydryl reactivity, and disulfide cross-linking. Adv. Prot. Chem. 63: 243-290.","pmid":"12629973","comments":null,"primary_structure_id":93},{"id":12,"ordering":12.0,"name":"","maintext":"Davison MD, and Findlay JBC (1986) Modification of ovine opsin with the photosensitive hydrophobic probe 1-azido-4-[125]-iodobenzene. Biochem. J. 234: 413-420.","pmid":"2941011","comments":null,"primary_structure_id":93},{"id":11,"ordering":11.0,"name":"","maintext":"Barclay P, and Findlay JBC (1984) Labelling of the cytoplasmic domains of ovine rhodopsin with hydrophilic chemical probes. Biochem. J. 220: 75-84.","pmid":"6378185","comments":null,"primary_structure_id":93},{"id":13,"ordering":13.0,"name":"","maintext":"Davison MD, and Findlay JBC (1986) Identification of the sites in opsin modified by photoactivated azido[125]iodobenzene. Biochem. J. 236: 389-395.","pmid":"2944512","comments":null,"primary_structure_id":93},{"id":15,"ordering":15.0,"name":"","maintext":"Krebs A, Edwards PC, Villa C, Li JD, and Schertler GFX (2003) The three-dimensional structure of bovine rhodopsin determined by electron cryomicroscopy. J. Biol. Chem. 278: 50217-50225.","pmid":"14514682","comments":null,"primary_structure_id":93},{"id":10,"ordering":10.0,"name":"","maintext":"Blaurock AE, and Wilkins MHF (1972) Structure of retinal photoreceptor membranes. Nature 236: 313-314.","pmid":"4552165","comments":null,"primary_structure_id":93}]}