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5DGY

Crystal structure of rhodopsin bound to visual arrestin

Functional Information from GO Data
ChainGOidnamespacecontents
A0000139cellular_componentGolgi membrane
A0000226biological_processmicrotubule cytoskeleton organization
A0001664molecular_functionG protein-coupled receptor binding
A0001750cellular_componentphotoreceptor outer segment
A0001917cellular_componentphotoreceptor inner segment
A0002031biological_processG protein-coupled receptor internalization
A0002046molecular_functionopsin binding
A0003796molecular_functionlysozyme activity
A0003824molecular_functioncatalytic activity
A0004930molecular_functionG protein-coupled receptor activity
A0005502molecular_function11-cis retinal binding
A0005515molecular_functionprotein binding
A0005794cellular_componentGolgi apparatus
A0005886cellular_componentplasma membrane
A0005911cellular_componentcell-cell junction
A0007165biological_processsignal transduction
A0007186biological_processG protein-coupled receptor signaling pathway
A0007601biological_processvisual perception
A0007602biological_processphototransduction
A0007603biological_processphototransduction, visible light
A0008020molecular_functionG protein-coupled photoreceptor activity
A0008152biological_processmetabolic process
A0009253biological_processpeptidoglycan catabolic process
A0009416biological_processresponse to light stimulus
A0009583biological_processdetection of light stimulus
A0009642biological_processresponse to light intensity
A0009881molecular_functionphotoreceptor activity
A0010467biological_processgene expression
A0016020cellular_componentmembrane
A0016038biological_processabsorption of visible light
A0016056biological_processrhodopsin mediated signaling pathway
A0016062biological_processobsolete adaptation of rhodopsin mediated signaling
A0016787molecular_functionhydrolase activity
A0016798molecular_functionhydrolase activity, acting on glycosyl bonds
A0016998biological_processcell wall macromolecule catabolic process
A0030430cellular_componenthost cell cytoplasm
A0030507molecular_functionspectrin binding
A0030660cellular_componentGolgi-associated vesicle membrane
A0031640biological_processkilling of cells of another organism
A0042622cellular_componentphotoreceptor outer segment membrane
A0042742biological_processdefense response to bacterium
A0042995cellular_componentcell projection
A0043052biological_processthermotaxis
A0044659biological_processviral release from host cell by cytolysis
A0045494biological_processphotoreceptor cell maintenance
A0046872molecular_functionmetal ion binding
A0050896biological_processresponse to stimulus
A0050953biological_processsensory perception of light stimulus
A0050960biological_processdetection of temperature stimulus involved in thermoception
A0051219molecular_functionphosphoprotein binding
A0060041biological_processretina development in camera-type eye
A0060170cellular_componentciliary membrane
A0060342cellular_componentphotoreceptor inner segment membrane
A0071482biological_processcellular response to light stimulus
A0071800biological_processpodosome assembly
A0097225cellular_componentsperm midpiece
A0097381cellular_componentphotoreceptor disc membrane
A0120200cellular_componentrod photoreceptor outer segment
A1904389biological_processrod bipolar cell differentiation
A1990913cellular_componentsperm head plasma membrane
B0000139cellular_componentGolgi membrane
B0000226biological_processmicrotubule cytoskeleton organization
B0001664molecular_functionG protein-coupled receptor binding
B0001750cellular_componentphotoreceptor outer segment
B0001917cellular_componentphotoreceptor inner segment
B0002031biological_processG protein-coupled receptor internalization
B0002046molecular_functionopsin binding
B0003796molecular_functionlysozyme activity
B0003824molecular_functioncatalytic activity
B0004930molecular_functionG protein-coupled receptor activity
B0005502molecular_function11-cis retinal binding
B0005515molecular_functionprotein binding
B0005794cellular_componentGolgi apparatus
B0005886cellular_componentplasma membrane
B0005911cellular_componentcell-cell junction
B0007165biological_processsignal transduction
B0007186biological_processG protein-coupled receptor signaling pathway
B0007601biological_processvisual perception
B0007602biological_processphototransduction
B0007603biological_processphototransduction, visible light
B0008020molecular_functionG protein-coupled photoreceptor activity
B0008152biological_processmetabolic process
B0009253biological_processpeptidoglycan catabolic process
B0009416biological_processresponse to light stimulus
B0009583biological_processdetection of light stimulus
B0009642biological_processresponse to light intensity
B0009881molecular_functionphotoreceptor activity
B0010467biological_processgene expression
B0016020cellular_componentmembrane
B0016038biological_processabsorption of visible light
B0016056biological_processrhodopsin mediated signaling pathway
B0016062biological_processobsolete adaptation of rhodopsin mediated signaling
B0016787molecular_functionhydrolase activity
B0016798molecular_functionhydrolase activity, acting on glycosyl bonds
B0016998biological_processcell wall macromolecule catabolic process
B0030430cellular_componenthost cell cytoplasm
B0030507molecular_functionspectrin binding
B0030660cellular_componentGolgi-associated vesicle membrane
B0031640biological_processkilling of cells of another organism
B0042622cellular_componentphotoreceptor outer segment membrane
B0042742biological_processdefense response to bacterium
B0042995cellular_componentcell projection
B0043052biological_processthermotaxis
B0044659biological_processviral release from host cell by cytolysis
B0045494biological_processphotoreceptor cell maintenance
B0046872molecular_functionmetal ion binding
B0050896biological_processresponse to stimulus
B0050953biological_processsensory perception of light stimulus
B0050960biological_processdetection of temperature stimulus involved in thermoception
B0051219molecular_functionphosphoprotein binding
B0060041biological_processretina development in camera-type eye
B0060170cellular_componentciliary membrane
B0060342cellular_componentphotoreceptor inner segment membrane
B0071482biological_processcellular response to light stimulus
B0071800biological_processpodosome assembly
B0097225cellular_componentsperm midpiece
B0097381cellular_componentphotoreceptor disc membrane
B0120200cellular_componentrod photoreceptor outer segment
B1904389biological_processrod bipolar cell differentiation
B1990913cellular_componentsperm head plasma membrane
C0000139cellular_componentGolgi membrane
C0000226biological_processmicrotubule cytoskeleton organization
C0001664molecular_functionG protein-coupled receptor binding
C0001750cellular_componentphotoreceptor outer segment
C0001917cellular_componentphotoreceptor inner segment
C0002031biological_processG protein-coupled receptor internalization
C0002046molecular_functionopsin binding
C0003796molecular_functionlysozyme activity
C0003824molecular_functioncatalytic activity
C0004930molecular_functionG protein-coupled receptor activity
C0005502molecular_function11-cis retinal binding
C0005515molecular_functionprotein binding
C0005794cellular_componentGolgi apparatus
C0005886cellular_componentplasma membrane
C0005911cellular_componentcell-cell junction
C0007165biological_processsignal transduction
C0007186biological_processG protein-coupled receptor signaling pathway
C0007601biological_processvisual perception
C0007602biological_processphototransduction
C0007603biological_processphototransduction, visible light
C0008020molecular_functionG protein-coupled photoreceptor activity
C0008152biological_processmetabolic process
C0009253biological_processpeptidoglycan catabolic process
C0009416biological_processresponse to light stimulus
C0009583biological_processdetection of light stimulus
C0009642biological_processresponse to light intensity
C0009881molecular_functionphotoreceptor activity
C0010467biological_processgene expression
C0016020cellular_componentmembrane
C0016038biological_processabsorption of visible light
C0016056biological_processrhodopsin mediated signaling pathway
C0016062biological_processobsolete adaptation of rhodopsin mediated signaling
C0016787molecular_functionhydrolase activity
C0016798molecular_functionhydrolase activity, acting on glycosyl bonds
C0016998biological_processcell wall macromolecule catabolic process
C0030430cellular_componenthost cell cytoplasm
C0030507molecular_functionspectrin binding
C0030660cellular_componentGolgi-associated vesicle membrane
C0031640biological_processkilling of cells of another organism
C0042622cellular_componentphotoreceptor outer segment membrane
C0042742biological_processdefense response to bacterium
C0042995cellular_componentcell projection
C0043052biological_processthermotaxis
C0044659biological_processviral release from host cell by cytolysis
C0045494biological_processphotoreceptor cell maintenance
C0046872molecular_functionmetal ion binding
C0050896biological_processresponse to stimulus
C0050953biological_processsensory perception of light stimulus
C0050960biological_processdetection of temperature stimulus involved in thermoception
C0051219molecular_functionphosphoprotein binding
C0060041biological_processretina development in camera-type eye
C0060170cellular_componentciliary membrane
C0060342cellular_componentphotoreceptor inner segment membrane
C0071482biological_processcellular response to light stimulus
C0071800biological_processpodosome assembly
C0097225cellular_componentsperm midpiece
C0097381cellular_componentphotoreceptor disc membrane
C0120200cellular_componentrod photoreceptor outer segment
C1904389biological_processrod bipolar cell differentiation
C1990913cellular_componentsperm head plasma membrane
D0000139cellular_componentGolgi membrane
D0000226biological_processmicrotubule cytoskeleton organization
D0001664molecular_functionG protein-coupled receptor binding
D0001750cellular_componentphotoreceptor outer segment
D0001917cellular_componentphotoreceptor inner segment
D0002031biological_processG protein-coupled receptor internalization
D0002046molecular_functionopsin binding
D0003796molecular_functionlysozyme activity
D0003824molecular_functioncatalytic activity
D0004930molecular_functionG protein-coupled receptor activity
D0005502molecular_function11-cis retinal binding
D0005515molecular_functionprotein binding
D0005794cellular_componentGolgi apparatus
D0005886cellular_componentplasma membrane
D0005911cellular_componentcell-cell junction
D0007165biological_processsignal transduction
D0007186biological_processG protein-coupled receptor signaling pathway
D0007601biological_processvisual perception
D0007602biological_processphototransduction
D0007603biological_processphototransduction, visible light
D0008020molecular_functionG protein-coupled photoreceptor activity
D0008152biological_processmetabolic process
D0009253biological_processpeptidoglycan catabolic process
D0009416biological_processresponse to light stimulus
D0009583biological_processdetection of light stimulus
D0009642biological_processresponse to light intensity
D0009881molecular_functionphotoreceptor activity
D0010467biological_processgene expression
D0016020cellular_componentmembrane
D0016038biological_processabsorption of visible light
D0016056biological_processrhodopsin mediated signaling pathway
D0016062biological_processobsolete adaptation of rhodopsin mediated signaling
D0016787molecular_functionhydrolase activity
D0016798molecular_functionhydrolase activity, acting on glycosyl bonds
D0016998biological_processcell wall macromolecule catabolic process
D0030430cellular_componenthost cell cytoplasm
D0030507molecular_functionspectrin binding
D0030660cellular_componentGolgi-associated vesicle membrane
D0031640biological_processkilling of cells of another organism
D0042622cellular_componentphotoreceptor outer segment membrane
D0042742biological_processdefense response to bacterium
D0042995cellular_componentcell projection
D0043052biological_processthermotaxis
D0044659biological_processviral release from host cell by cytolysis
D0045494biological_processphotoreceptor cell maintenance
D0046872molecular_functionmetal ion binding
D0050896biological_processresponse to stimulus
D0050953biological_processsensory perception of light stimulus
D0050960biological_processdetection of temperature stimulus involved in thermoception
D0051219molecular_functionphosphoprotein binding
D0060041biological_processretina development in camera-type eye
D0060170cellular_componentciliary membrane
D0060342cellular_componentphotoreceptor inner segment membrane
D0071482biological_processcellular response to light stimulus
D0071800biological_processpodosome assembly
D0097225cellular_componentsperm midpiece
D0097381cellular_componentphotoreceptor disc membrane
D0120200cellular_componentrod photoreceptor outer segment
D1904389biological_processrod bipolar cell differentiation
D1990913cellular_componentsperm head plasma membrane
Functional Information from PROSITE/UniProt
site_idPS00295
Number of Residues19
DetailsARRESTINS Arrestins signature. FRYGqEDiDVMGLtFrRDL
ChainResidueDetails
APHE1066-LEU1084

site_idPS00237
Number of Residues17
DetailsG_PROTEIN_RECEP_F1_1 G-protein coupled receptors family 1 signature. IALwSLVVLAIERYVvV
ChainResidueDetails
AILE123-VAL139

site_idPS00238
Number of Residues17
DetailsOPSIN Visual pigments (opsins) retinal binding site. IPaFfAKSAAiyNPviY
ChainResidueDetails
AILE290-TYR306

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues4
DetailsACT_SITE: Proton donor/acceptor => ECO:0000255|HAMAP-Rule:MF_04110, ECO:0000269|PubMed:3382407, ECO:0000269|PubMed:7831309, ECO:0000269|PubMed:8266098
ChainResidueDetails
AGLU-150
BGLU-150
CGLU-150
DGLU-150

site_idSWS_FT_FI2
Number of Residues4
DetailsACT_SITE: Proton donor/acceptor => ECO:0000255|HAMAP-Rule:MF_04110, ECO:0000269|PubMed:1892846, ECO:0000269|PubMed:3382407, ECO:0000269|PubMed:7831309, ECO:0000269|PubMed:8266098
ChainResidueDetails
AASP-141
BASP-141
CASP-141
DASP-141

site_idSWS_FT_FI3
Number of Residues8
DetailsBINDING: BINDING => ECO:0000269|PubMed:8266098
ChainResidueDetails
ALEU-129
APHE-57
BLEU-129
BPHE-57
CLEU-129
CPHE-57
DLEU-129
DPHE-57

site_idSWS_FT_FI4
Number of Residues8
DetailsBINDING: BINDING => ECO:0000303|PubMed:7831309
ChainResidueDetails
ASER-44
AASN-29
BSER-44
BASN-29
CSER-44
CASN-29
DSER-44
DASN-29

site_idSWS_FT_FI5
Number of Residues340
DetailsTOPO_DOM: Extracellular => ECO:0000269|PubMed:26200343, ECO:0000269|PubMed:28753425
ChainResidueDetails
AMET1-GLN36
CTHR97-CYS110
CGLY174-SER202
CILE275-GLY284
DMET1-GLN36
DTHR97-CYS110
DGLY174-SER202
DILE275-GLY284
ATHR97-CYS110
AGLY174-SER202
AILE275-GLY284
BMET1-GLN36
BTHR97-CYS110
BGLY174-SER202
BILE275-GLY284
CMET1-GLN36

site_idSWS_FT_FI6
Number of Residues96
DetailsTRANSMEM: Helical; Name=1 => ECO:0000269|PubMed:26200343, ECO:0000269|PubMed:28753425
ChainResidueDetails
APHE37-VAL61
BPHE37-VAL61
CPHE37-VAL61
DPHE37-VAL61

site_idSWS_FT_FI7
Number of Residues376
DetailsTOPO_DOM: Cytoplasmic => ECO:0000269|PubMed:26200343, ECO:0000269|PubMed:28753425
ChainResidueDetails
ATHR62-ASN73
CGLU134-HIS152
CGLN225-ARG252
CASN310-ALA994
DTHR62-ASN73
DGLU134-HIS152
DGLN225-ARG252
DASN310-ALA994
AGLU134-HIS152
AGLN225-ARG252
AASN310-ALA994
BTHR62-ASN73
BGLU134-HIS152
BGLN225-ARG252
BASN310-ALA994
CTHR62-ASN73

site_idSWS_FT_FI8
Number of Residues88
DetailsTRANSMEM: Helical; Name=2 => ECO:0000269|PubMed:26200343, ECO:0000269|PubMed:28753425
ChainResidueDetails
ATYR74-TYR96
BTYR74-TYR96
CTYR74-TYR96
DTYR74-TYR96

site_idSWS_FT_FI9
Number of Residues88
DetailsTRANSMEM: Helical; Name=3 => ECO:0000269|PubMed:26200343, ECO:0000269|PubMed:28753425
ChainResidueDetails
AASN111-ILE133
BASN111-ILE133
CASN111-ILE133
DASN111-ILE133

site_idSWS_FT_FI10
Number of Residues80
DetailsTRANSMEM: Helical; Name=4 => ECO:0000269|PubMed:26200343, ECO:0000269|PubMed:28753425
ChainResidueDetails
AALA153-ALA173
BALA153-ALA173
CALA153-ALA173
DALA153-ALA173

site_idSWS_FT_FI11
Number of Residues84
DetailsTRANSMEM: Helical; Name=5 => ECO:0000269|PubMed:26200343, ECO:0000269|PubMed:28753425
ChainResidueDetails
APHE203-GLY224
BPHE203-GLY224
CPHE203-GLY224
DPHE203-GLY224

site_idSWS_FT_FI12
Number of Residues84
DetailsTRANSMEM: Helical; Name=6 => ECO:0000269|PubMed:26200343, ECO:0000269|PubMed:28753425
ChainResidueDetails
AMET253-TYR274
BMET253-TYR274
CMET253-TYR274
DMET253-TYR274

site_idSWS_FT_FI13
Number of Residues96
DetailsTRANSMEM: Helical; Name=7 => ECO:0000269|PubMed:26200343, ECO:0000269|PubMed:28753425
ChainResidueDetails
APRO285-MET309
BPRO285-MET309
CPRO285-MET309
DPRO285-MET309

site_idSWS_FT_FI14
Number of Residues8
DetailsBINDING: BINDING => ECO:0000250|UniProtKB:P02699
ChainResidueDetails
AGLU201
AGLN279
BGLU201
BGLN279
CGLU201
CGLN279
DGLU201
DGLN279

site_idSWS_FT_FI15
Number of Residues4
DetailsSITE: Plays an important role in the conformation switch to the active conformation => ECO:0000269|PubMed:26200343
ChainResidueDetails
AGLN113
BGLN113
CGLN113
DGLN113

site_idSWS_FT_FI16
Number of Residues4
DetailsMOD_RES: N-acetylmethionine => ECO:0000250|UniProtKB:P02699
ChainResidueDetails
AMET1
BMET1
CMET1
DMET1

site_idSWS_FT_FI17
Number of Residues4
DetailsMOD_RES: N6-(retinylidene)lysine => ECO:0000250|UniProtKB:P02699
ChainResidueDetails
ALYS296
BLYS296
CLYS296
DLYS296

site_idSWS_FT_FI18
Number of Residues8
DetailsMOD_RES: Phosphoserine => ECO:0000269|PubMed:28753425
ChainResidueDetails
ASER980
ASER984
BSER980
BSER984
CSER980
CSER984
DSER980
DSER984

site_idSWS_FT_FI19
Number of Residues4
DetailsMOD_RES: Phosphothreonine => ECO:0000269|PubMed:28753425
ChainResidueDetails
ATHR982
BTHR982
CTHR982
DTHR982

site_idSWS_FT_FI20
Number of Residues8
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P02699
ChainResidueDetails
ATHR986
ATHR988
BTHR986
BTHR988
CTHR986
CTHR988
DTHR986
DTHR988

site_idSWS_FT_FI21
Number of Residues4
DetailsMOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P02699
ChainResidueDetails
ASER989
BSER989
CSER989
DSER989

site_idSWS_FT_FI22
Number of Residues8
DetailsLIPID: S-palmitoyl cysteine => ECO:0000250|UniProtKB:P02699
ChainResidueDetails
ACYS322
ACYS323
BCYS322
BCYS323
CCYS322
CCYS323
DCYS322
DCYS323

site_idSWS_FT_FI23
Number of Residues4
DetailsCARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000250|UniProtKB:P02699
ChainResidueDetails
ACYS2
BCYS2
CCYS2
DCYS2

site_idSWS_FT_FI24
Number of Residues4
DetailsCARBOHYD: N-linked (GlcNAc...) asparagine => ECO:0000269|PubMed:28753425
ChainResidueDetails
AASN15
BASN15
CASN15
DASN15

site_idSWS_FT_FI25
Number of Residues4
DetailsMOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P15887
ChainResidueDetails
ATHR1231
BTHR1231
CTHR1231
DTHR1231

Catalytic Information from CSA
site_idMCSA1
Number of Residues2
DetailsM-CSA 921
ChainResidueDetails
AGLU-150proton shuttle (general acid/base)
AASP-141covalent catalysis

site_idMCSA2
Number of Residues2
DetailsM-CSA 921
ChainResidueDetails
BGLU-150proton shuttle (general acid/base)
BASP-141covalent catalysis

site_idMCSA3
Number of Residues2
DetailsM-CSA 921
ChainResidueDetails
CGLU-150proton shuttle (general acid/base)
CASP-141covalent catalysis

site_idMCSA4
Number of Residues2
DetailsM-CSA 921
ChainResidueDetails
DGLU-150proton shuttle (general acid/base)
DASP-141covalent catalysis

218853

数据于2024-04-24公开中

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