1F88 - JenaLib

Asym.Unit - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BOVINE RHODOPSIN

Authors :   T. Okada, K. Palczewski, R. E. Stenkamp, M. Miyano

Date :   29 Jun 00 (Deposition) - 04 Aug 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Photoreceptor, G Protein-Coupled Receptor, Membrane Protein, Retinal Protein, Visual Pigment, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Palczewski, T. Kumasaka, T. Hori, C. A. Behnke, H. Motoshima, B. A. Fox, I. Le Trong, D. C. Teller, T. Okada, R. E. Stenkamp, M. Yamamoto, M. Miyano
Crystal Structure Of Rhodopsin: A G Protein-Coupled Receptor.
Science V. 289 739 2000
PubMed-ID: 10926528 | Reference-DOI: 10.1126/SCIENCE.289.5480.739

Molecule 1 - RHODOPSIN
	Chains	:	A, B
	Organ	:	RETINA
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Other Details	:	BOVINE RETINA, ROD CELL OUTER SEGMENTS

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 21)

No.	Name	Count	Type	Full Name
1	HG	6	Ligand/Ion	MERCURY (II) ION
2	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	8	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	RET	2	Ligand/Ion	RETINAL
5	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 11)

No.	Name	Count	Type	Full Name
1	HG	-1	Ligand/Ion	MERCURY (II) ION
2	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	8	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	RET	2	Ligand/Ion	RETINAL
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 5)

No.	Name	Count	Type	Full Name
1	HG	-1	Ligand/Ion	MERCURY (II) ION
2	MAN	-1	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	RET	1	Ligand/Ion	RETINAL
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (3, 6)

No.	Name	Count	Type	Full Name
1	HG	-1	Ligand/Ion	MERCURY (II) ION
2	MAN	1	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	RET	1	Ligand/Ion	RETINAL
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (21, 21)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	THR A:4 , ASN A:15 , GLY A:18 , VAL A:20 , ARG A:21 , NAG A:502 , LYS B:16 , NAG B:601	BINDING SITE FOR RESIDUE NAG A 501
02	AC2	SOFTWARE	ARG A:21 , NAG A:501 , LYS B:16	BINDING SITE FOR RESIDUE NAG A 502
03	AC3	SOFTWARE	NAG A:501 , THR B:4 , ASN B:15 , GLY B:18 , VAL B:20 , ARG B:21 , NAG B:602	BINDING SITE FOR RESIDUE NAG B 601
04	AC4	SOFTWARE	LYS A:16 , ARG B:21 , NAG B:601 , MAN B:603	BINDING SITE FOR RESIDUE NAG B 602
05	AC5	SOFTWARE	NAG B:602	BINDING SITE FOR RESIDUE MAN B 603
06	AC6	SOFTWARE	MET A:1 , ASN A:2 , GLY A:280 , SER A:281 , ASP A:282 , NAG A:702 , HOH A:953 , ZN B:909	BINDING SITE FOR RESIDUE NAG A 701
07	AC7	SOFTWARE	NAG A:701	BINDING SITE FOR RESIDUE NAG A 702
08	AC8	SOFTWARE	ASN B:2 , GLY B:280 , SER B:281 , ASP B:282 , NAG B:802	BINDING SITE FOR RESIDUE NAG B 801
09	AC9	SOFTWARE	NAG B:801	BINDING SITE FOR RESIDUE NAG B 802
10	BC1	SOFTWARE	CYS A:264 , THR A:297	BINDING SITE FOR RESIDUE HG A 901
11	BC2	SOFTWARE	ALA B:260 , CYS B:264 , THR B:297	BINDING SITE FOR RESIDUE HG B 902
12	BC3	SOFTWARE	ALA A:132 , CYS A:222 , TYR A:223 , LEU A:226	BINDING SITE FOR RESIDUE HG A 903
13	BC4	SOFTWARE	ALA B:132 , CYS B:222 , TYR B:223 , LEU B:226	BINDING SITE FOR RESIDUE HG B 904
14	BC5	SOFTWARE	GLN A:312 , CYS A:316 , SER A:338	BINDING SITE FOR RESIDUE HG A 905
15	BC6	SOFTWARE	HIS B:65 , CYS B:316	BINDING SITE FOR RESIDUE HG B 906
16	BC7	SOFTWARE	GLU A:201 , GLN A:279 , GLU B:196	BINDING SITE FOR RESIDUE ZN A 907
17	BC8	SOFTWARE	GLU A:196 , PHE B:276 , GLN B:279	BINDING SITE FOR RESIDUE ZN B 908
18	BC9	SOFTWARE	NAG A:701 , PRO B:7 , HIS B:195	BINDING SITE FOR RESIDUE ZN B 909
19	CC1	SOFTWARE	LYS A:311 , ARG A:314	BINDING SITE FOR RESIDUE ZN A 910
20	CC2	SOFTWARE	ALA A:117 , THR A:118 , GLY A:121 , GLU A:122 , SER A:186 , CYS A:187 , MET A:207 , PHE A:212 , TRP A:265 , TYR A:268 , ALA A:269 , ALA A:292 , LYS A:296	BINDING SITE FOR RESIDUE RET A 977
21	CC3	SOFTWARE	ALA B:117 , THR B:118 , GLY B:121 , GLU B:122 , CYS B:187 , ILE B:189 , MET B:207 , PHE B:212 , PHE B:261 , TYR B:268 , ALA B:269 , ALA B:292 , LYS B:296	BINDING SITE FOR RESIDUE RET B 978

Asymmetric Unit

No.	Residues
1	A:110	-	A:187
2	B:110	-	B:187

(no "Cis Peptide Bond" information available for 1F88)

(no "SAP(SNP)/Variant" information available for 1F88)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F1_1	PS00237	G-protein coupled receptors family 1 signature.	OPSD_BOVIN	123-139	2	A:123-139 B:123-139
2	OPSIN	PS00238	Visual pigments (opsins) retinal binding site.	OPSD_BOVIN	290-306	2	A:290-306 B:290-306

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F1_1	PS00237	G-protein coupled receptors family 1 signature.	OPSD_BOVIN	123-139	2	A:123-139 B:123-139
2	OPSIN	PS00238	Visual pigments (opsins) retinal binding site.	OPSD_BOVIN	290-306	2	A:290-306 B:290-306

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F1_1	PS00237	G-protein coupled receptors family 1 signature.	OPSD_BOVIN	123-139	1	A:123-139 -
2	OPSIN	PS00238	Visual pigments (opsins) retinal binding site.	OPSD_BOVIN	290-306	1	A:290-306 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F1_1	PS00237	G-protein coupled receptors family 1 signature.	OPSD_BOVIN	123-139	1	- B:123-139
2	OPSIN	PS00238	Visual pigments (opsins) retinal binding site.	OPSD_BOVIN	290-306	1	- B:290-306

Asymmetric Unit (5, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENSBTAT00000001730	1	ENSBTAE00000013842	chr22:57733705-57733336	370	OPSD_BOVIN	1-124	124	2	A:1-124 B:1-124	124 124
1.2	ENSBTAT00000001730	2	ENSBTAE00000013843	chr22:57731646-57731478	169	OPSD_BOVIN	124-180	57	2	A:124-180 B:124-180 (gaps)	57 57
1.3	ENSBTAT00000001730	3	ENSBTAE00000013844	chr22:57730259-57730094	166	OPSD_BOVIN	180-235	56	2	A:180-235 B:180-226	56 47
1.4	ENSBTAT00000001730	4	ENSBTAE00000013845	chr22:57729975-57729736	240	OPSD_BOVIN	236-315	80	2	A:240-315 B:243-315	76 73
1.5	ENSBTAT00000001730	5	ENSBTAE00000326840	chr22:57728876-57728766	111	OPSD_BOVIN	316-351	36	2	A:316-348 (gaps) B:316-326	33 11

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:338
 aligned with OPSD_BOVIN | P02699 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:348
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340        
           OPSD_BOVIN     1 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNPLGDDEASTTVSKTETSQVAPA 348
               SCOP domains d1f88a_ A: Rhodopsin                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1f88A00 A:1-348 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee....ee................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh....eeee....eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.........----.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....------............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F------------------------------------------------------------------------------------------------------------------------------------------------------OPSIN            ------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:1-124 UniProt: 1-124                                                                                       -------------------------------------------------------Exon 1.3  PDB: A:180-235 UniProt: 180-235               Exon 1.4  PDB: A:240-315 UniProt: 236-315 [INCOMPLETE]                          Exon 1.5  PDB: A:316-348 (gaps)   Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------Exon 1.2  PDB: A:124-180 UniProt: 124-180                ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1f88 A   1 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAA----SATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKNP------STTVSKTETSQVAPA 348
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230    |  240       250       260       270       280       290       300       310       320      |  -   |   340        
                                                                                                                                                                                                                                                                    235  240                                                                                    327    334

Chain B from PDB  Type:PROTEIN  Length:305
 aligned with OPSD_BOVIN | P02699 from UniProtKB/Swiss-Prot  Length:348

    Alignment length:326
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320      
           OPSD_BOVIN     1 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKPMSNFRFGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKN 326
               SCOP domains d1f88b_ B: Rhodopsin                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1f88B00 B:1-326 Rhopdopsin 7-helix transmembrane proteins                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....ee.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....-----....hhhhhhhhhhhhhhhhhhhhhhh...eeee....eeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhh.----------------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F------------------------------------------------------------------------------------------------------------------------------------------------------OPSIN            -------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:1-124 UniProt: 1-124                                                                                       -------------------------------------------------------Exon 1.3  PDB: B:180-226 UniProt: 180-235 [INCOMPLETE]  Exon 1.4  PDB: B:243-315 UniProt: 236-315 [INCOMPLETE]                          Exon 1.5    Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------Exon 1.2  PDB: B:124-180 (gaps) UniProt: 124-180         -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1f88 B   1 MNGTEGPNFYVPFSNKTGVVRSPFEAPQYYLAEPWQFSMLAAYMFLLIMLGFPINFLTLYVTVQHKKLRTPLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVCKP-----FGENHAIMGVAFTWVMALACAAPPLVGWSRYIPEGMQCSCGIDYYTPHEETNNESFVIYMFVVHFIIPLIVIFFCYGQL----------------TQKAEKEVTRMVIIMVIAFLICWLPYAGVAFYIFTHQGSDFGPIFMTIPAFFAKTSAVYNPVIYIMMNKQFRNCMVTTLCCGKN 326
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140 |     150       160       170       180       190       200       210       220     |   -         -  |    250       260       270       280       290       300       310       320      
                                                                                                                                                                       142   148                                                                           226              243

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Membrane and cell surface proteins and peptides (2046)

Fold: Family A G protein-coupled receptor-like (138)

Superfamily: Family A G protein-coupled receptor-like (138)

Family: Rhodopsin-like (16)

Protein domain: Rhodopsin (8)

Cow (Bos taurus) [TaxId: 9913] (8)

1a	d1f88a_	A:
1b	d1f88b_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Rhopdopsin 7-helix transmembrane proteins (128)

Homologous Superfamily: Rhopdopsin 7-helix transmembrane proteins (128)

Cattle (Bos taurus) (9)

1a	1f88B00	B:1-326
1b	1f88A00	A:1-348

(no "Pfam Domain" information available for 1F88)

Asymmetric Unit(hide GO term definitions)

Chain A,B (OPSD_BOVIN | P02699)

molecular function
	GO:0008020	G-protein coupled photoreceptor activity	Combining with incidental electromagnetic radiation, particularly visible light, and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
	GO:0004930	G-protein coupled receptor activity	Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
	GO:0005085	guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0009881	photoreceptor activity	The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0016038	absorption of visible light	The reception of a (visible light) photon by a cell, visible light being defined as having a wavelength within the range 380-780 nm.
	GO:0071482	cellular response to light stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
	GO:0009583	detection of light stimulus	The series of events in which a light stimulus (in the form of photons) is received and converted into a molecular signal.
	GO:0045494	photoreceptor cell maintenance	Any process preventing the degeneration of the photoreceptor, a specialized cell type that is sensitive to light.
	GO:0007602	phototransduction	The sequence of reactions within a cell required to convert absorbed photons into a molecular signal.
	GO:0007603	phototransduction, visible light	The sequence of reactions within a cell required to convert absorbed photons from visible light into a molecular signal. A visible light stimulus is electromagnetic radiation that can be perceived visually by an organism; for organisms lacking a visual system, this can be defined as light with a wavelength within the range 380 to 780 nm.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
	GO:0022400	regulation of rhodopsin mediated signaling pathway	Any process that modulates the frequency, rate or extent of rhodopsin-mediated signaling.
	GO:0009416	response to light stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
	GO:0050896	response to stimulus	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0060041	retina development in camera-type eye	The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
	GO:0016056	rhodopsin mediated signaling pathway	The series of molecular signals generated as a consequence of excitation of rhodopsin by a photon and the events that convert the absorbed photons into a cellular response.
	GO:0050953	sensory perception of light stimulus	The series of events required for an organism to receive a sensory light stimulus, convert it to a molecular signal, and recognize and characterize the signal. This is a neurological process.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0007601	visual perception	The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
	GO:0005794	Golgi apparatus	A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
	GO:0000139	Golgi membrane	The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
	GO:0005911	cell-cell junction	A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0097381	photoreceptor disc membrane	Ovally-shaped membranous stack located inside the photoreceptor outer segment, and containing densely packed molecules of the photoreceptor protein rhodopsin that traverse the lipid bilayer. Disc membranes are apparently derived from the plasma membrane in the region of the cilium that connects the photoreceptor outer segment to the inner segment.
	GO:0001917	photoreceptor inner segment	The inner segment of a vertebrate photoreceptor containing mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs.
	GO:0060342	photoreceptor inner segment membrane	The membrane surrounding the inner segment of a vertebrate photoreceptor. The photoreceptor inner segment contains mitochondria, ribosomes and membranes where opsin molecules are assembled and passed to be part of the outer segment discs.
	GO:0001750	photoreceptor outer segment	The outer segment of a vertebrate photoreceptor that contains discs of photoreceptive membranes.
	GO:0042622	photoreceptor outer segment membrane	The membrane surrounding the outer segment of a vertebrate photoreceptor.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		HG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MAN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		RET	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1f88)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)
Insightii
	retinal environment; all amino acids are shown that have an atom within a distance of 4 Angstrom from any of the retinal atoms; coloring of amino acids corresponds to the helix coloring shown above; only one chain shown [ mono GIF format \| stereo GIF format ]
Weblab
	retinal environment; only one chain shown [ mono JPG format \| stereo JPG format ]
	protein: ribbon, secondary structure, chain-specific coloring; retinal: spacefill: other ligands: balls and sticks [ mono GIF format ]
	protein: ribbon, secondary structure; retinal: spacefill: other ligands: balls and sticks; one chain as transparent surface [ mono GIF format ]
	protein: ribbon, secondary structure, sticks; retinal: spacefill; other ligands: balls and sticks [ mono GIF format ]
	spacefill, chain-specific coloring [ mono GIF format ]
Prepi
	protein: ribbon, secondary structure; ligands: spacefill; two chains [ mono GIF format \| stereo GIF format ]
	protein: ribbon, secondary structure; ligands: spacefill; two chains [ mono GIF format \| stereo GIF format ]
	protein: ribbon, secondary structure, sticks; ligands: spacefill; two chains [ mono GIF format \| stereo GIF format ]
	spacefill, chain-specific coloring; two chains [ mono GIF format \| stereo GIF format ]

Access by PDB/NDB ID
	1f88
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	OPSD_BOVIN \| P02699
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	OPSD_BOVIN \| P02699
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 1F88)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 21)

Sites (21, 21)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (5, 10)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (37, 37)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File