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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  THEORETICAL MODEL OF RED CONE PIGMENT
 
Authors :  R. E. Stenkamp, S. Filipek, C. A. G. G. Driessen, D. C. Teller, K. Palczewski
Date :  03 Jan 02  (Deposition) - 16 Jan 02  (Release) - 11 Dec 02  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Red Cone Pigment, Longwavelength Photoreceptor, G Protein- Coupled Receptor, Membrane Protein, Retinal Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. E. Stenkamp, S. Filipek, C. A. G. G. Driessen, D. C. Teller, K. Palczewski
Crystal Structure Of Rhodopsin: A Template For Cone Visual Pigments And Other G Protein-Coupled Receptors
Biochim. Biophys. Acta V. 1565 168 2002
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RED CONE PIGMENT
    ChainsA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymRED-SENSITIVE OPSIN, RED CONE PHOTORECEPTOR PIGMENT

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Theoretical Model (1, 1)
No.NameCountTypeFull Name
1RET1Ligand/IonRETINAL

(-) Sites  (0, 0)

(no "Site" information available for 1KPX)

(-) SS Bonds  (1, 1)

Theoretical Model
No.Residues
1A:126 -A:203

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (13, 13)

Theoretical Model (13, 13)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_012009T65IOPSR_HUMANPolymorphism1065419AT65I
02UniProtVAR_012010I111VOPSR_HUMANPolymorphism1065421AI111V
03UniProtVAR_012011S116YOPSR_HUMANPolymorphism1065422AS116Y
04UniProtVAR_012012L153MOPSR_HUMANPolymorphism713AL153M
05UniProtVAR_012013A174VOPSR_HUMANPolymorphism731613AA174V
06UniProtVAR_004842S180AOPSR_HUMANPolymorphism949431AS180A
07UniProtVAR_009298C203ROPSR_HUMANDisease (BCM)  ---AC203R
08UniProtVAR_012014I230TOPSR_HUMANPolymorphism1065425AI230T
09UniProtVAR_050612I274VOPSR_HUMANPolymorphism2315122AI274V
10UniProtVAR_012015A298POPSR_HUMANPolymorphism1065440AA298P
11UniProtVAR_009299P307LOPSR_HUMANDisease (BCM)  ---AP307L
12UniProtVAR_012016Y309FOPSR_HUMANPolymorphism1065441AY309F
13UniProtVAR_064054G338EOPSR_HUMANDisease (CBP)  ---AG338E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Theoretical Model (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1G_PROTEIN_RECEP_F1_1PS00237 G-protein coupled receptors family 1 signature.OPSR_HUMAN139-155  1A:139-155
2OPSINPS00238 Visual pigments (opsins) retinal binding site.OPSR_HUMAN306-322  1A:306-322

(-) Exons   (6, 6)

Theoretical Model (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003699511aENSE00001833335X:153409698-153409869172OPSR_HUMAN1-38381A:1-3838
1.2ENST000003699512ENSE00001646397X:153416128-153416424297OPSR_HUMAN38-1371001A:38-137100
1.3aENST000003699513aENSE00001736878X:153418413-153418581169OPSR_HUMAN137-193571A:137-19357
1.4ENST000003699514ENSE00001788298X:153420049-153420214166OPSR_HUMAN193-248561A:193-24856
1.5cENST000003699515cENSE00001634443X:153421769-153422008240OPSR_HUMAN249-328801A:249-32880
1.6bENST000003699516bENSE00001842369X:153424291-153424507217OPSR_HUMAN329-364361A:329-36436

(-) Sequences/Alignments

Theoretical Model
   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:364
 aligned with OPSR_HUMAN | P04000 from UniProtKB/Swiss-Prot  Length:364

    Alignment length:364
                                    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       350       360    
           OPSR_HUMAN     1 MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISIVNQVSGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNVRFDAKLAIVGIAFSWIWSAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIMLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAANPGYAFHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSSVSPA 364
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee............eee.....................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh...eeee....eeee.........hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------I---------------------------------------------V----Y------------------------------------M--------------------V-----A----------------------R--------------------------T-------------------------------------------V-----------------------P--------L-F----------------------------E-------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F------------------------------------------------------------------------------------------------------------------------------------------------------OPSIN            ------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:1-38 UniProt: 1-38  --------------------------------------------------------------------------------------------------Exon 1.3a  PDB: A:137-193 UniProt: 137-193               -------------------------------------------------------Exon 1.5c  PDB: A:249-328 UniProt: 249-328                                      Exon 1.6b  PDB: A:329-364            Transcript 1 (1)
           Transcript 1 (2) -------------------------------------Exon 1.2  PDB: A:38-137 UniProt: 38-137                                                             -------------------------------------------------------Exon 1.4  PDB: A:193-248 UniProt: 193-248               -------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1kpx A   1 MAQQWSLQRLAGRHPQDSYEDSTQSSIFTYTNSNSTRGPFEGPNYHIAPRWVYHLTSVWMIFVVTASVFTNGLVLAATMKFKKLRHPLNWILVNLAVADLAETVIASTISIVNQVSGYFVLGHPMCVLEGYTVSLCGITGLWSLAIISWERWLVVCKPFGNVRFDAKLAIVGIAFSWIWSAVWTAPPIFGWSRYWPHGLKTSCGPDVFSGSSYPGVQSYMIVLMVTCCIIPLAIIMLCYLQVWLAIRAVAKQQKESESTQKAEKEVTRMVVVMIFAYCVCWGPYTFFACFAAANPGYAFHPLMAALPAYFAKSATIYNPVIYVFMNRQFRNCILQLFGKKVDDGSELSSASKTEVSSVSSVSPA 364
                                    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       350       360    

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 1KPX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1KPX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (19, 19)

Theoretical Model(hide GO term definitions)
Chain A   (OPSR_HUMAN | P04000)
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: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: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: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:0009584    detection of visible light    The series of events in which a visible light stimulus is received by a cell and converted 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:0007602    phototransduction    The sequence of reactions within a cell required to convert absorbed photons into a molecular signal.
    GO:0032467    positive regulation of cytokinesis    Any process that activates or increases the frequency, rate or extent of the division of the cytoplasm of a cell, and its separation into two daughter cells.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
    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:0001523    retinoid metabolic process    The chemical reactions and pathways involving retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.
    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: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: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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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(-) Related Entries Specified in the PDB File

1f88 1F88 IS RHODOPSIN.
1hzx 1HZX IS RHODOPSIN.