Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

8A6E

100 picosecond light activated crystal structure of bovine rhodopsin in Lipidic Cubic Phase (SACLA)

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	0016062	biological_process	obsolete adaptation of rhodopsin mediated signaling
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	0016062	biological_process	obsolete adaptation of rhodopsin mediated signaling
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	ILE524-VAL540

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

Chain	Residue	Details
A	ILE691-TYR707

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	MET402-GLN437
A	THR498-CYS511
A	GLY575-SER603
A	ILE676-ILE687
B	MET402-GLN437
B	THR498-CYS511
B	GLY575-SER603
B	ILE676-ILE687

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	PHE438-VAL462
B	PHE438-VAL462

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	THR463-ASN474
A	GLU535-HIS553
A	GLN626-ARG653
A	MET710-ALA749
B	THR463-ASN474
B	GLU535-HIS553
B	GLN626-ARG653
B	MET710-ALA749

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	TYR475-TYR497
B	TYR475-TYR497

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	ASN512-ILE534
B	ASN512-ILE534

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	ALA554-VAL574
B	ALA554-VAL574

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	PHE604-GLY625
B	PHE604-GLY625

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	MET654-TYR675
B	MET654-TYR675

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	PHE688-MET709
B	PHE688-MET709

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	GLU602
A	GLN680
B	GLU602
B	GLN680

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	GLU514
B	GLU514

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

Chain	Residue	Details
A	MET402
B	MET402

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	LYS697
B	LYS697

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	SER735
A	SER739
B	SER735
B	SER739

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	THR736
A	THR737
A	THR741
A	THR743
B	THR736
B	THR737
B	THR741
B	THR743

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	SER744
B	SER744

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	CYS723
B	CYS723

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	CYS724
B	CYS724

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	ASN403
B	ASN403

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	ASN416
B	ASN416

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)