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(-) Description

Title :  THEORETICAL MODEL OF THE CELLULAR RETINALDEHYDE BINDING PROTEIN IN ITS CLOSED CONFORMATION
 
Authors :  T. Liu, E. Jenwitheesuk, D. C. Teller, R. Samudrala
Date :  17 Sep 04  (Deposition) - 30 Aug 05  (Release) - 06 Sep 05  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Cralbp (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Liu, E. Jenwitheesuk, D. C. Teller, R. Samudrala
Structural Insights Into The Cellular Retinaldehyde-Binding Protein (Cralbp)
Proteins V. 61 412 2005
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CELLULAR RETINALDEHYDE-BINDING PROTEIN
    ChainsA
    FragmentCRAL-TRIO DOMAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymCRALBP

 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 1XGG)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XGG)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Theoretical Model (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_005140R151QRLBP1_HUMANDisease (RPA)28933989AR150Q
2UniProtVAR_037317M226KRLBP1_HUMANDisease (RPA)137853291AM225K
3UniProtVAR_015172R234WRLBP1_HUMANDisease (BRD)28933990AR233W

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

(-) PROSITE Motifs  (1, 1)

Theoretical Model (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRAL_TRIOPS50191 CRAL-TRIO lipid binding domain profile.RLBP1_HUMAN136-297  1A:135-294

(-) Exons   (5, 5)

Theoretical Model (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002681251ENSE00001391768chr15:89764922-89764766157RLBP1_HUMAN-00--
1.2ENST000002681252ENSE00001375615chr15:89763090-89762968123RLBP1_HUMAN-00--
1.3ENST000002681253ENSE00001386450chr15:89762306-89762195112RLBP1_HUMAN1-440--
1.4ENST000002681254ENSE00000943552chr15:89761924-89761796129RLBP1_HUMAN5-47430--
1.5ENST000002681255ENSE00000943553chr15:89760555-89760351205RLBP1_HUMAN48-116691A:66-11550
1.6ENST000002681256ENSE00000943554chr15:89758469-89758291179RLBP1_HUMAN116-175601A:115-17460
1.7ENST000002681257ENSE00000943555chr15:89755132-89754974159RLBP1_HUMAN176-228531A:175-22753
1.8ENST000002681258ENSE00000943556chr15:89754040-89753930111RLBP1_HUMAN229-265371A:228-26437
1.9ENST000002681259ENSE00000943557chr15:89753674-89753098577RLBP1_HUMAN266-317521A:265-29430

(-) 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:229
 aligned with RLBP1_HUMAN | P12271 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:229
                                    76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286         
          RLBP1_HUMAN    67 QEMVQAQAASGEELAVAVAERVQEKDSGFFLRFIRARKFNVGRAYELLRGYVNFRLQYPELFDSLSPEAVRCTIEAGYPGVLSSRDKYGRVVMLFNIENWQSQEITFDEILQAYCFILEKLLENEETQINGFCIIENFKGFTMQQAASLRTSDLRKMVDMLQDSFPARFKAIHFIHQPWYFTTTYNVVKPFLKSKLLERVFVHGDDLSGFYQEIDENILPSDFGGTLPK 295
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhh......eee.........eeeeee.........hhhhhhhhhhhhhhhhh.hhhhhhhheeeeee....hhhhhhhhhhhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhhhhh.eee....hhhhhh.......hhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------Q--------------------------------------------------------------------------K-------W------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------CRAL_TRIO  PDB: A:135-294 UniProt: 136-297                                                                                                                       PROSITE
           Transcript 1 (1) Exon 1.5  PDB: A:66-115 UniProt: 48-116           -----------------------------------------------------------Exon 1.7  PDB: A:175-227 UniProt: 176-228            Exon 1.8  PDB: A:228-264             Exon 1.9  PDB: A:265-294       Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------Exon 1.6  PDB: A:115-174 UniProt: 116-175                   ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 1xgg A  66 QEMVQAQAASGEELAVAVAERVQEKDSGFFLRFIRARKFNVGRAYELLRGYVNFRLQYPELFDSLSPEAVRCTIEAGYPGVLSSRDKYGRVVMLFNIENWQSQEITFDEILQAYCFILEKLLENEETQINGFCIIENFKGFTMQQAASLRTSDLRKMVDMLQDSFPARFKAIHFIHQPWYFTTTYNVVKPFLKSKLLERVFVHGDDLSGFYQEIDENILPSDFGGTLPK 294
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285         

   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 1XGG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Theoretical Model(hide GO term definitions)
Chain A   (RLBP1_HUMAN | P12271)
molecular function
    GO:0005502    11-cis retinal binding    Interacting selectively and non-covalently with 11-cis retinal, an isomer of retinal that plays an important role in the visual process in most vertebrates. 11-cis retinal combines with opsin in the rods (scotopsin) to form rhodopsin or visual purple. Retinal is one of the three compounds that makes up vitamin A.
    GO:0016918    retinal binding    Interacting selectively and non-covalently with retinal, one of the forms of vitamin A. Retinal plays an important role in the visual process in most vertebrates, combining with opsins to form visual pigments in the retina.
    GO:0019841    retinol binding    Interacting selectively and non-covalently with retinol, vitamin A1, 2,6,6-trimethyl-1-(9'-hydroxy-3',7'-dimethylnona-1',3',5',7'-tetraenyl)cyclohex-1-ene, one of the three components that makes up vitamin A. Retinol is an intermediate in the vision cycle and it also plays a role in growth and differentiation.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    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:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    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.
    GO:0006776    vitamin A metabolic process    The chemical reactions and pathways involving any of the vitamin A compounds, retinol, retinal (retinaldehyde) and retinoic acid, all of which are derivatives of beta-carotene.
cellular component
    GO:0044297    cell body    The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RLBP1_HUMAN | P122711xgh 3hx3 3hy5 4ciz 4cj6

(-) Related Entries Specified in the PDB File

1xgh THEORETICAL MODEL OF THE CELLULAR RETINALDEHYDE BINDING PROTEIN IN ITS OPEN CONFORMATION