Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1F88

CRYSTAL STRUCTURE OF BOVINE RHODOPSIN

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000139	cellular_component	Golgi membrane
A	0000226	biological_process	microtubule cytoskeleton organization
A	0001750	cellular_component	photoreceptor outer segment
A	0001917	cellular_component	photoreceptor inner segment
A	0001965	molecular_function	G-protein alpha-subunit binding
A	0002046	molecular_function	opsin binding
A	0004930	molecular_function	G protein-coupled receptor activity
A	0005085	molecular_function	guanyl-nucleotide exchange factor activity
A	0005502	molecular_function	11-cis retinal binding
A	0005515	molecular_function	protein binding
A	0005794	cellular_component	Golgi apparatus
A	0005886	cellular_component	plasma membrane
A	0005911	cellular_component	cell-cell junction
A	0007186	biological_process	G protein-coupled receptor signaling pathway
A	0007601	biological_process	visual perception
A	0007602	biological_process	phototransduction
A	0007603	biological_process	phototransduction, visible light
A	0008020	molecular_function	G protein-coupled photoreceptor activity
A	0008270	molecular_function	zinc ion binding
A	0009416	biological_process	response to light stimulus
A	0009583	biological_process	detection of light stimulus
A	0009642	biological_process	response to light intensity
A	0009881	molecular_function	photoreceptor activity
A	0010467	biological_process	gene expression
A	0016020	cellular_component	membrane
A	0016038	biological_process	absorption of visible light
A	0016056	biological_process	G protein-coupled opsin signaling pathway
A	0019867	cellular_component	outer membrane
A	0042622	cellular_component	photoreceptor outer segment membrane
A	0042802	molecular_function	identical protein binding
A	0042995	cellular_component	cell projection
A	0043052	biological_process	thermotaxis
A	0045494	biological_process	photoreceptor cell maintenance
A	0046872	molecular_function	metal ion binding
A	0050953	biological_process	sensory perception of light stimulus
A	0050960	biological_process	detection of temperature stimulus involved in thermoception
A	0060041	biological_process	retina development in camera-type eye
A	0060342	cellular_component	photoreceptor inner segment membrane
A	0071482	biological_process	cellular response to light stimulus
A	0071800	biological_process	podosome assembly
A	0097225	cellular_component	sperm midpiece
A	0097381	cellular_component	photoreceptor disc membrane
A	0097648	cellular_component	G protein-coupled receptor complex
A	0120200	cellular_component	rod photoreceptor outer segment
A	1904389	biological_process	rod bipolar cell differentiation
A	1990763	molecular_function	arrestin family protein binding
A	1990913	cellular_component	sperm head plasma membrane
B	0000139	cellular_component	Golgi membrane
B	0000226	biological_process	microtubule cytoskeleton organization
B	0001750	cellular_component	photoreceptor outer segment
B	0001917	cellular_component	photoreceptor inner segment
B	0001965	molecular_function	G-protein alpha-subunit binding
B	0002046	molecular_function	opsin binding
B	0004930	molecular_function	G protein-coupled receptor activity
B	0005085	molecular_function	guanyl-nucleotide exchange factor activity
B	0005502	molecular_function	11-cis retinal binding
B	0005515	molecular_function	protein binding
B	0005794	cellular_component	Golgi apparatus
B	0005886	cellular_component	plasma membrane
B	0005911	cellular_component	cell-cell junction
B	0007186	biological_process	G protein-coupled receptor signaling pathway
B	0007601	biological_process	visual perception
B	0007602	biological_process	phototransduction
B	0007603	biological_process	phototransduction, visible light
B	0008020	molecular_function	G protein-coupled photoreceptor activity
B	0008270	molecular_function	zinc ion binding
B	0009416	biological_process	response to light stimulus
B	0009583	biological_process	detection of light stimulus
B	0009642	biological_process	response to light intensity
B	0009881	molecular_function	photoreceptor activity
B	0010467	biological_process	gene expression
B	0016020	cellular_component	membrane
B	0016038	biological_process	absorption of visible light
B	0016056	biological_process	G protein-coupled opsin signaling pathway
B	0019867	cellular_component	outer membrane
B	0042622	cellular_component	photoreceptor outer segment membrane
B	0042802	molecular_function	identical protein binding
B	0042995	cellular_component	cell projection
B	0043052	biological_process	thermotaxis
B	0045494	biological_process	photoreceptor cell maintenance
B	0046872	molecular_function	metal ion binding
B	0050953	biological_process	sensory perception of light stimulus
B	0050960	biological_process	detection of temperature stimulus involved in thermoception
B	0060041	biological_process	retina development in camera-type eye
B	0060342	cellular_component	photoreceptor inner segment membrane
B	0071482	biological_process	cellular response to light stimulus
B	0071800	biological_process	podosome assembly
B	0097225	cellular_component	sperm midpiece
B	0097381	cellular_component	photoreceptor disc membrane
B	0097648	cellular_component	G protein-coupled receptor complex
B	0120200	cellular_component	rod photoreceptor outer segment
B	1904389	biological_process	rod bipolar cell differentiation
B	1990763	molecular_function	arrestin family protein binding
B	1990913	cellular_component	sperm head plasma membrane

Functional Information from PROSITE/UniProt

site_id	PS00237
Number of Residues	17
Details	G_PROTEIN_RECEP_F1_1 G-protein coupled receptors family 1 signature. IALwSLVVLAIERYVvV

Chain	Residue	Details
A	ILE123-VAL139

site_id	PS00238
Number of Residues	17
Details	OPSIN Visual pigments (opsins) retinal binding site. IPaFfAKTSAvyNPviY

Chain	Residue	Details
A	ILE290-TYR306

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	174
Details	TOPO_DOM: Extracellular => ECO:0000269\|PubMed:10926528, ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:11972040, ECO:0000269\|PubMed:12044163, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:15491621, ECO:0000269\|PubMed:16586416, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:17060607, ECO:0000269\|PubMed:17449675, ECO:0000269\|PubMed:17825322, ECO:0000269\|PubMed:18563085, ECO:0000269\|PubMed:18645239, ECO:0000269\|PubMed:18818650, ECO:0000269\|PubMed:21389983, ECO:0000269\|PubMed:22198838, ECO:0000269\|PubMed:23579341, ECO:0000269\|PubMed:25205354, ECO:0000269\|PubMed:26526852, ECO:0000269\|PubMed:27458239

Chain	Residue	Details
A	MET1-GLN36
A	THR97-CYS110
A	GLY174-SER202
A	ILE275-ILE286
B	MET1-GLN36
B	THR97-CYS110
B	GLY174-SER202
B	ILE275-ILE286

site_id	SWS_FT_FI2
Number of Residues	48
Details	TRANSMEM: Helical; Name=1 => ECO:0000269\|PubMed:10926528, ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:11972040, ECO:0000269\|PubMed:12044163, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:15491621, ECO:0000269\|PubMed:16586416, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:17060607, ECO:0000269\|PubMed:17449675, ECO:0000269\|PubMed:17825322, ECO:0000269\|PubMed:18563085, ECO:0000269\|PubMed:18645239, ECO:0000269\|PubMed:18818650, ECO:0000269\|PubMed:21389983, ECO:0000269\|PubMed:22198838, ECO:0000269\|PubMed:23579341, ECO:0000269\|PubMed:25205354, ECO:0000269\|PubMed:26526852, ECO:0000269\|PubMed:27458239

Chain	Residue	Details
A	PHE37-VAL61
B	PHE37-VAL61

site_id	SWS_FT_FI3
Number of Residues	190
Details	TOPO_DOM: Cytoplasmic => ECO:0000269\|PubMed:10926528, ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:11972040, ECO:0000269\|PubMed:12044163, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:15491621, ECO:0000269\|PubMed:16586416, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:17060607, ECO:0000269\|PubMed:17449675, ECO:0000269\|PubMed:17825322, ECO:0000269\|PubMed:18563085, ECO:0000269\|PubMed:18645239, ECO:0000269\|PubMed:18818650, ECO:0000269\|PubMed:21389983, ECO:0000269\|PubMed:22198838, ECO:0000269\|PubMed:23579341, ECO:0000269\|PubMed:25205354, ECO:0000269\|PubMed:26526852, ECO:0000269\|PubMed:27458239

Chain	Residue	Details
A	THR62-ASN73
A	GLU134-HIS152
A	GLN225-ARG252
A	MET309-ALA348
B	THR62-ASN73
B	GLU134-HIS152
B	GLN225-ARG252
B	MET309-ALA348

site_id	SWS_FT_FI4
Number of Residues	44
Details	TRANSMEM: Helical; Name=2 => ECO:0000269\|PubMed:10926528, ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:11972040, ECO:0000269\|PubMed:12044163, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:15491621, ECO:0000269\|PubMed:16586416, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:17060607, ECO:0000269\|PubMed:17449675, ECO:0000269\|PubMed:17825322, ECO:0000269\|PubMed:18563085, ECO:0000269\|PubMed:18645239, ECO:0000269\|PubMed:18818650, ECO:0000269\|PubMed:21389983, ECO:0000269\|PubMed:22198838, ECO:0000269\|PubMed:23579341, ECO:0000269\|PubMed:25205354, ECO:0000269\|PubMed:26526852, ECO:0000269\|PubMed:27458239

Chain	Residue	Details
A	TYR74-TYR96
B	TYR74-TYR96

site_id	SWS_FT_FI5
Number of Residues	44
Details	TRANSMEM: Helical; Name=3 => ECO:0000269\|PubMed:10926528, ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:11972040, ECO:0000269\|PubMed:12044163, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:15491621, ECO:0000269\|PubMed:16586416, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:17060607, ECO:0000269\|PubMed:17449675, ECO:0000269\|PubMed:17825322, ECO:0000269\|PubMed:18563085, ECO:0000269\|PubMed:18645239, ECO:0000269\|PubMed:18818650, ECO:0000269\|PubMed:21389983, ECO:0000269\|PubMed:22198838, ECO:0000269\|PubMed:23579341, ECO:0000269\|PubMed:25205354, ECO:0000269\|PubMed:26526852, ECO:0000269\|PubMed:27458239

Chain	Residue	Details
A	ASN111-ILE133
B	ASN111-ILE133

site_id	SWS_FT_FI6
Number of Residues	40
Details	TRANSMEM: Helical; Name=4 => ECO:0000269\|PubMed:10926528, ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:11972040, ECO:0000269\|PubMed:12044163, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:15491621, ECO:0000269\|PubMed:16586416, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:17060607, ECO:0000269\|PubMed:17449675, ECO:0000269\|PubMed:17825322, ECO:0000269\|PubMed:18563085, ECO:0000269\|PubMed:18645239, ECO:0000269\|PubMed:18818650, ECO:0000269\|PubMed:21389983, ECO:0000269\|PubMed:22198838, ECO:0000269\|PubMed:23579341, ECO:0000269\|PubMed:25205354, ECO:0000269\|PubMed:26526852, ECO:0000269\|PubMed:27458239

Chain	Residue	Details
A	ALA153-VAL173
B	ALA153-VAL173

site_id	SWS_FT_FI7
Number of Residues	42
Details	TRANSMEM: Helical; Name=5 => ECO:0000269\|PubMed:10926528, ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:11972040, ECO:0000269\|PubMed:12044163, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:15491621, ECO:0000269\|PubMed:16586416, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:17060607, ECO:0000269\|PubMed:17449675, ECO:0000269\|PubMed:17825322, ECO:0000269\|PubMed:18563085, ECO:0000269\|PubMed:18645239, ECO:0000269\|PubMed:18818650, ECO:0000269\|PubMed:21389983, ECO:0000269\|PubMed:22198838, ECO:0000269\|PubMed:23579341, ECO:0000269\|PubMed:25205354, ECO:0000269\|PubMed:26526852, ECO:0000269\|PubMed:27458239

Chain	Residue	Details
A	PHE203-GLY224
B	PHE203-GLY224

site_id	SWS_FT_FI8
Number of Residues	42
Details	TRANSMEM: Helical; Name=6 => ECO:0000269\|PubMed:10926528, ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:11972040, ECO:0000269\|PubMed:12044163, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:15491621, ECO:0000269\|PubMed:16586416, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:17060607, ECO:0000269\|PubMed:17449675, ECO:0000269\|PubMed:17825322, ECO:0000269\|PubMed:18563085, ECO:0000269\|PubMed:18645239, ECO:0000269\|PubMed:18818650, ECO:0000269\|PubMed:21389983, ECO:0000269\|PubMed:22198838, ECO:0000269\|PubMed:23579341, ECO:0000269\|PubMed:25205354, ECO:0000269\|PubMed:26526852, ECO:0000269\|PubMed:27458239

Chain	Residue	Details
A	MET253-TYR274
B	MET253-TYR274

site_id	SWS_FT_FI9
Number of Residues	42
Details	TRANSMEM: Helical; Name=7 => ECO:0000269\|PubMed:10926528, ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:11972040, ECO:0000269\|PubMed:12044163, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:15491621, ECO:0000269\|PubMed:16586416, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:17060607, ECO:0000269\|PubMed:17449675, ECO:0000269\|PubMed:17825322, ECO:0000269\|PubMed:18563085, ECO:0000269\|PubMed:18645239, ECO:0000269\|PubMed:18818650, ECO:0000269\|PubMed:21389983, ECO:0000269\|PubMed:22198838, ECO:0000269\|PubMed:23579341, ECO:0000269\|PubMed:25205354, ECO:0000269\|PubMed:26526852, ECO:0000269\|PubMed:27458239

Chain	Residue	Details
A	PHE287-MET308
B	PHE287-MET308

site_id	SWS_FT_FI10
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:10926528, ECO:0000269\|PubMed:11425302, ECO:0007744\|PDB:1F88, ECO:0007744\|PDB:1HZX

Chain	Residue	Details
A	GLU201
A	GLN279
B	GLU201
B	GLN279

site_id	SWS_FT_FI11
Number of Residues	2
Details	SITE: Plays an important role in the conformation switch to the active conformation => ECO:0000269\|PubMed:21389983, ECO:0000305\|PubMed:22198838, ECO:0000305\|PubMed:23579341, ECO:0000305\|PubMed:27458239

Chain	Residue	Details
A	GLU113
B	GLU113

site_id	SWS_FT_FI12
Number of Residues	2
Details	MOD_RES: N-acetylmethionine => ECO:0000305\|PubMed:6759163

Chain	Residue	Details
A	MET1
B	MET1

site_id	SWS_FT_FI13
Number of Residues	2
Details	MOD_RES: N6-(retinylidene)lysine => ECO:0000269\|PubMed:10926528, ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:11972040, ECO:0000269\|PubMed:12044163, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:15491621, ECO:0000269\|PubMed:16586416, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:17449675, ECO:0000269\|PubMed:22198838, ECO:0000269\|PubMed:23303210, ECO:0000269\|PubMed:27458239, ECO:0000269\|PubMed:6870827, ECO:0000305\|PubMed:6759163, ECO:0007744\|PDB:1F88, ECO:0007744\|PDB:1GZM, ECO:0007744\|PDB:1HZX, ECO:0007744\|PDB:1JFP, ECO:0007744\|PDB:2HPY, ECO:0007744\|PDB:3C9L, ECO:0007744\|PDB:3OAX, ECO:0007744\|PDB:3PQR, ECO:0007744\|PDB:3PXO, ECO:0007744\|PDB:5DYS

Chain	Residue	Details
A	LYS296
B	LYS296

site_id	SWS_FT_FI14
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000269\|PubMed:15111114, ECO:0000269\|PubMed:15351781

Chain	Residue	Details
A	SER334
A	SER338
B	SER334
B	SER338

site_id	SWS_FT_FI15
Number of Residues	8
Details	MOD_RES: Phosphothreonine => ECO:0000269\|PubMed:15111114, ECO:0000269\|PubMed:15351781

Chain	Residue	Details
A	THR335
A	THR336
A	THR340
A	THR342
B	THR335
B	THR336
B	THR340
B	THR342

site_id	SWS_FT_FI16
Number of Residues	2
Details	MOD_RES: Phosphoserine; by RK and GRK7 => ECO:0000269\|PubMed:1396673, ECO:0000269\|PubMed:15111114, ECO:0000269\|PubMed:15351781

Chain	Residue	Details
A	SER343
B	SER343

site_id	SWS_FT_FI17
Number of Residues	2
Details	LIPID: S-palmitoyl cysteine => ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:11972040, ECO:0000269\|PubMed:1512231, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:18818650, ECO:0000269\|PubMed:21389983, ECO:0000269\|PubMed:22198838, ECO:0000269\|PubMed:26526852, ECO:0000269\|PubMed:27458239, ECO:0000269\|PubMed:3350146, ECO:0007744\|PDB:1HZX, ECO:0007744\|PDB:1L9H, ECO:0007744\|PDB:2HPY, ECO:0007744\|PDB:4X1H, ECO:0007744\|PDB:5DYS

Chain	Residue	Details
A	CYS322
B	CYS322

site_id	SWS_FT_FI18
Number of Residues	2
Details	LIPID: S-palmitoyl cysteine => ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:11972040, ECO:0000269\|PubMed:1512231, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:18818650, ECO:0000269\|PubMed:21389983, ECO:0000269\|PubMed:22198838, ECO:0000269\|PubMed:23579341, ECO:0000269\|PubMed:25205354, ECO:0000269\|PubMed:26526852, ECO:0000269\|PubMed:27458239, ECO:0000269\|PubMed:3350146, ECO:0007744\|PDB:1HZX, ECO:0007744\|PDB:1L9H, ECO:0007744\|PDB:2HPY, ECO:0007744\|PDB:4BEY, ECO:0007744\|PDB:4PXF, ECO:0007744\|PDB:4X1H, ECO:0007744\|PDB:5DYS

Chain	Residue	Details
A	CYS323
B	CYS323

site_id	SWS_FT_FI19
Number of Residues	2
Details	CARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:15491621, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:18818650, ECO:0000269\|PubMed:26526852, ECO:0000269\|PubMed:468821, ECO:0000269\|PubMed:6759163, ECO:0007744\|PDB:1F88, ECO:0007744\|PDB:1GZM, ECO:0007744\|PDB:1HZX, ECO:0007744\|PDB:1U19, ECO:0007744\|PDB:2G87, ECO:0007744\|PDB:2HPY, ECO:0007744\|PDB:2I35, ECO:0007744\|PDB:2I36, ECO:0007744\|PDB:2I37, ECO:0007744\|PDB:2PED, ECO:0007744\|PDB:3C9L, ECO:0007744\|PDB:3CAP, ECO:0007744\|PDB:3DQB, ECO:0007744\|PDB:3OAX, ECO:0007744\|PDB:3PQR, ECO:0007744\|PDB:3PXO, ECO:0007744\|PDB:4X1H

Chain	Residue	Details
A	ASN2
B	ASN2

site_id	SWS_FT_FI20
Number of Residues	2
Details	CARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000269\|PubMed:11425302, ECO:0000269\|PubMed:11972040, ECO:0000269\|PubMed:15327956, ECO:0000269\|PubMed:15491621, ECO:0000269\|PubMed:16908857, ECO:0000269\|PubMed:18818650, ECO:0000269\|PubMed:21389983, ECO:0000269\|PubMed:22198838, ECO:0000269\|PubMed:23579341, ECO:0000269\|PubMed:25205354, ECO:0000269\|PubMed:26526852, ECO:0000269\|PubMed:468821, ECO:0000269\|PubMed:6759163, ECO:0007744\|PDB:1F88, ECO:0007744\|PDB:1GZM, ECO:0007744\|PDB:1HZX, ECO:0007744\|PDB:1L9H, ECO:0007744\|PDB:1U19, ECO:0007744\|PDB:2G87, ECO:0007744\|PDB:2HPY, ECO:0007744\|PDB:2I35, ECO:0007744\|PDB:2I36, ECO:0007744\|PDB:2I37, ECO:0007744\|PDB:2J4Y, ECO:0007744\|PDB:2PED, ECO:0007744\|PDB:2X72, ECO:0007744\|PDB:3C9L, ECO:0007744\|PDB:3C9M, ECO:0007744\|PDB:3CAP, ECO:0007744\|PDB:3DQB, ECO:0007744\|PDB:3OAX, ECO:0007744\|PDB:3PQR, ECO:0007744\|PDB:3PXO, ECO:0007744\|PDB:4A4M, ECO:0007744\|PDB:4BEY, ECO:0007744\|PDB:4BEZ, ECO:0007744\|PDB:4J4Q, ECO:0007744\|PDB:4PXF, ECO:0007744\|PDB:4X1H, ECO:0007744\|PDB:5DYS, ECO:0007744\|PDB:5EN0, ECO:0007744\|PDB:5TE3

Chain	Residue	Details
A	ASN15
B	ASN15

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)