OPSD_TODPA
ID OPSD_TODPA Reviewed; 448 AA.
AC P31356;
DT 01-JUL-1993, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 104.
DE RecName: Full=Rhodopsin;
GN Name=RHO;
OS Todarodes pacificus (Japanese flying squid) (Ommastrephes pacificus).
OC Eukaryota; Metazoa; Spiralia; Lophotrochozoa; Mollusca; Cephalopoda;
OC Coleoidea; Decapodiformes; Teuthida; Oegopsina; Ommastrephidae; Todarodes.
OX NCBI_TaxID=6637;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], AND PROTEIN SEQUENCE OF 2-17; 129-140 AND
RP 303-313.
RC TISSUE=Retina;
RX PubMed=8428633; DOI=10.1016/0014-5793(93)81480-n;
RA Hara-Nishimura I., Kondo M., Nishimura M., Hara R., Hara T.;
RT "Cloning and nucleotide sequence of cDNA for rhodopsin of the squid
RT Todarodes pacificus.";
RL FEBS Lett. 317:5-11(1993).
RN [2]
RP PROTEIN SEQUENCE OF 303-313, AND RETINAL-CHROMOPHORE BINDING AT LYS-305.
RX PubMed=3191148; DOI=10.1016/0167-4838(88)90289-0;
RA Seidou M., Kubota I., Hiraki K., Kito Y.;
RT "Amino acid sequence of the retinal binding site of squid visual pigment.";
RL Biochim. Biophys. Acta 957:318-321(1988).
RN [3]
RP FUNCTION, CRYSTALLIZATION, TISSUE SPECIFICITY, AND SUBCELLULAR LOCATION.
RX PubMed=17554166; DOI=10.1107/s1744309107017423;
RA Murakami M., Kitahara R., Gotoh T., Kouyama T.;
RT "Crystallization and crystal properties of squid rhodopsin.";
RL Acta Crystallogr. F 63:475-479(2007).
RN [4] {ECO:0007744|PDB:2ZIY}
RP X-RAY CRYSTALLOGRAPHY (3.70 ANGSTROMS) OF 2-373 IN COMPLEX WITH
RP ALL-TRANS-RETINAL, FUNCTION, DISULFIDE BONDS, SUBCELLULAR LOCATION,
RP TOPOLOGY, TISSUE SPECIFICITY, IDENTIFICATION BY MASS SPECTROMETRY, AND
RP PALMITOYLATION AT CYS-336 AND CYS-337.
RX PubMed=18463093; DOI=10.1074/jbc.c800040200;
RA Shimamura T., Hiraki K., Takahashi N., Hori T., Ago H., Masuda K.,
RA Takio K., Ishiguro M., Miyano M.;
RT "Crystal structure of squid rhodopsin with intracellularly extended
RT cytoplasmic region.";
RL J. Biol. Chem. 283:17753-17756(2008).
RN [5] {ECO:0007744|PDB:2Z73}
RP X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS) IN COMPLEX WITH ALL-TRANS-RETINAL,
RP FUNCTION, SUBCELLULAR LOCATION, TISSUE SPECIFICITY, PALMITOYLATION AT
RP CYS-337, GLYCOSYLATION AT ASN-8, DISULFIDE BONDS, AND TOPOLOGY.
RX PubMed=18480818; DOI=10.1038/nature06925;
RA Murakami M., Kouyama T.;
RT "Crystal structure of squid rhodopsin.";
RL Nature 453:363-367(2008).
RN [6] {ECO:0007744|PDB:3AYM, ECO:0007744|PDB:3AYN}
RP X-RAY CRYSTALLOGRAPHY (2.70 ANGSTROMS) IN COMPLEX WITH ALL-TRANS-RETINAL,
RP FUNCTION, AND DISULFIDE BONDS.
RX PubMed=21906602; DOI=10.1016/j.jmb.2011.08.044;
RA Murakami M., Kouyama T.;
RT "Crystallographic analysis of the primary photochemical reaction of squid
RT rhodopsin.";
RL J. Mol. Biol. 413:615-627(2011).
RN [7] {ECO:0007744|PDB:4WW3}
RP X-RAY CRYSTALLOGRAPHY (2.80 ANGSTROMS) OF 9-358 IN COMPLEX WITH
RP ALL-TRANS-RETINAL, FUNCTION, AND DISULFIDE BONDS.
RX PubMed=26024518; DOI=10.1371/journal.pone.0126970;
RA Murakami M., Kouyama T.;
RT "Crystallographic Study of the LUMI Intermediate of Squid Rhodopsin.";
RL PLoS ONE 10:E0126970-E0126970(2015).
CC -!- FUNCTION: Photoreceptor required for image-forming vision at low light
CC intensity (Probable). Light-induced isomerization of 11-cis to all-
CC trans retinal triggers a conformational change that activates signaling
CC via G-proteins. Signaling mediates the activation of phospholipase C
CC (Probable). Subsequent receptor phosphorylation mediates displacement
CC of the bound G-protein alpha subunit by arrestin and terminates
CC signaling (By similarity). {ECO:0000250|UniProtKB:P08100, ECO:0000305,
CC ECO:0000305|PubMed:17554166, ECO:0000305|PubMed:18463093,
CC ECO:0000305|PubMed:18480818, ECO:0000305|PubMed:21906602,
CC ECO:0000305|PubMed:26024518}.
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000269|PubMed:17554166,
CC ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818,
CC ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518}; Multi-pass
CC membrane protein {ECO:0000269|PubMed:18463093,
CC ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
CC ECO:0000269|PubMed:26024518}. Note=Detected on the rhabdomere membrane
CC in the photoreceptor outer segment. {ECO:0000269|PubMed:17554166,
CC ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818,
CC ECO:0000269|PubMed:21906602}.
CC -!- TISSUE SPECIFICITY: Retina, rhabdomere membrane (at protein level).
CC {ECO:0000269|PubMed:17554166, ECO:0000269|PubMed:18463093,
CC ECO:0000269|PubMed:18480818}.
CC -!- PTM: Contains one covalently linked retinal chromophore. Upon light
CC absorption, the covalently bound 11-cis-retinal is converted to all-
CC trans-retinal (PubMed:3191148, PubMed:17554166, PubMed:18463093,
CC PubMed:18480818, PubMed:21906602). After hydrolysis of the Schiff base
CC and release of the covalently bound all-trans-retinal, active rhodopsin
CC is regenerated by binding of a fresh molecule of 11-cis-retinal (By
CC similarity). {ECO:0000250|UniProtKB:P02699,
CC ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818,
CC ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518,
CC ECO:0000269|PubMed:3191148}.
CC -!- SIMILARITY: Belongs to the G-protein coupled receptor 1 family. Opsin
CC subfamily. {ECO:0000255|PROSITE-ProRule:PRU00521}.
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DR EMBL; X70498; CAA49906.1; -; mRNA.
DR PIR; S29483; S29483.
DR PDB; 2Z73; X-ray; 2.50 A; A/B=1-448.
DR PDB; 2ZIY; X-ray; 3.70 A; A=2-373.
DR PDB; 3AYM; X-ray; 2.80 A; A/B=1-448.
DR PDB; 3AYN; X-ray; 2.70 A; A/B=1-448.
DR PDB; 4WW3; X-ray; 2.80 A; A/B=9-358.
DR PDBsum; 2Z73; -.
DR PDBsum; 2ZIY; -.
DR PDBsum; 3AYM; -.
DR PDBsum; 3AYN; -.
DR PDBsum; 4WW3; -.
DR AlphaFoldDB; P31356; -.
DR SMR; P31356; -.
DR DIP; DIP-60624N; -.
DR GlyConnect; 524; 4 N-Linked glycans.
DR iPTMnet; P31356; -.
DR PRIDE; P31356; -.
DR EvolutionaryTrace; P31356; -.
DR GO; GO:0016021; C:integral component of membrane; IDA:UniProtKB.
DR GO; GO:0005886; C:plasma membrane; ISS:UniProtKB.
DR GO; GO:0004930; F:G protein-coupled receptor activity; IEA:UniProtKB-KW.
DR GO; GO:0009881; F:photoreceptor activity; IEA:UniProtKB-KW.
DR GO; GO:0016918; F:retinal binding; IDA:UniProtKB.
DR GO; GO:0007602; P:phototransduction; IEA:UniProtKB-KW.
DR GO; GO:0007601; P:visual perception; IEA:UniProtKB-KW.
DR InterPro; IPR000276; GPCR_Rhodpsn.
DR InterPro; IPR017452; GPCR_Rhodpsn_7TM.
DR InterPro; IPR001760; Opsin.
DR InterPro; IPR027430; Retinal_BS.
DR InterPro; IPR006031; XYPPX.
DR Pfam; PF00001; 7tm_1; 1.
DR Pfam; PF02162; XYPPX; 5.
DR PRINTS; PR00237; GPCRRHODOPSN.
DR PRINTS; PR00238; OPSIN.
DR SMART; SM01381; 7TM_GPCR_Srsx; 1.
DR PROSITE; PS00237; G_PROTEIN_RECEP_F1_1; 1.
DR PROSITE; PS50262; G_PROTEIN_RECEP_F1_2; 1.
DR PROSITE; PS00238; OPSIN; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Chromophore; Direct protein sequencing; Disulfide bond;
KW G-protein coupled receptor; Glycoprotein; Lipoprotein; Membrane; Palmitate;
KW Phosphoprotein; Photoreceptor protein; Receptor; Retinal protein;
KW Sensory transduction; Transducer; Transmembrane; Transmembrane helix;
KW Vision.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:8428633"
FT CHAIN 2..448
FT /note="Rhodopsin"
FT /id="PRO_0000197748"
FT TOPO_DOM 2..33
FT /note="Extracellular"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TRANSMEM 34..58
FT /note="Helical; Name=1"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TOPO_DOM 59..70
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TRANSMEM 71..97
FT /note="Helical; Name=2"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TOPO_DOM 98..109
FT /note="Extracellular"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TRANSMEM 110..131
FT /note="Helical; Name=3"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TOPO_DOM 132..151
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TRANSMEM 152..172
FT /note="Helical; Name=4"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TOPO_DOM 173..199
FT /note="Extracellular"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TRANSMEM 200..224
FT /note="Helical; Name=5"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TOPO_DOM 225..261
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TRANSMEM 262..283
FT /note="Helical; Name=6"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TOPO_DOM 284..293
FT /note="Extracellular"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TRANSMEM 294..315
FT /note="Helical; Name=7"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT TOPO_DOM 316..448
FT /note="Cytoplasmic"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518"
FT REGION 343..448
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 390..436
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 305
FT /note="N6-(retinylidene)lysine"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602,
FT ECO:0000269|PubMed:26024518, ECO:0000269|PubMed:3191148,
FT ECO:0007744|PDB:2Z73, ECO:0007744|PDB:4WW3"
FT LIPID 336
FT /note="S-palmitoyl cysteine"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0007744|PDB:2ZIY"
FT LIPID 337
FT /note="S-palmitoyl cysteine"
FT /evidence="ECO:0000269|PubMed:18463093,
FT ECO:0000269|PubMed:18480818, ECO:0007744|PDB:2ZIY"
FT CARBOHYD 8
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000305|PubMed:18463093"
FT DISULFID 108..186
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00521,
FT ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818,
FT ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518,
FT ECO:0007744|PDB:2Z73, ECO:0007744|PDB:2ZIY,
FT ECO:0007744|PDB:3AYM, ECO:0007744|PDB:3AYN,
FT ECO:0007744|PDB:4WW3"
FT STRAND 15..17
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 21..24
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 31..61
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 63..65
FT /evidence="ECO:0007829|PDB:4WW3"
FT HELIX 70..87
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 91..97
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 104..136
FT /evidence="ECO:0007829|PDB:2Z73"
FT TURN 141..143
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 149..167
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 169..172
FT /evidence="ECO:0007829|PDB:2Z73"
FT STRAND 177..179
FT /evidence="ECO:0007829|PDB:2Z73"
FT STRAND 183..188
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 195..207
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 210..224
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 227..238
FT /evidence="ECO:0007829|PDB:2Z73"
FT TURN 239..241
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 246..286
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 289..291
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 294..306
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 307..309
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 311..318
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 320..329
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 331..334
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 341..344
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 345..351
FT /evidence="ECO:0007829|PDB:2Z73"
FT HELIX 355..357
FT /evidence="ECO:0007829|PDB:4WW3"
SQ SEQUENCE 448 AA; 49836 MW; B48D56A1D057492A CRC64;
MGRDLRDNET WWYNPSIVVH PHWREFDQVP DAVYYSLGIF IGICGIIGCG GNGIVIYLFT
KTKSLQTPAN MFIINLAFSD FTFSLVNGFP LMTISCFLKK WIFGFAACKV YGFIGGIFGF
MSIMTMAMIS IDRYNVIGRP MAASKKMSHR RAFIMIIFVW LWSVLWAIGP IFGWGAYTLE
GVLCNCSFDY ISRDSTTRSN ILCMFILGFF GPILIIFFCY FNIVMSVSNH EKEMAAMAKR
LNAKELRKAQ AGANAEMRLA KISIVIVSQF LLSWSPYAVV ALLAQFGPLE WVTPYAAQLP
VMFAKASAIH NPMIYSVSHP KFREAISQTF PWVLTCCQFD DKETEDDKDA ETEIPAGESS
DAAPSADAAQ MKEMMAMMQK MQQQQAAYPP QGYAPPPQGY PPQGYPPQGY PPQGYPPQGY
PPPPQGAPPQ GAPPAAPPQG VDNQAYQA
