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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COMPLEX OF THE CELLULAR RETINAL BINDING PROTEIN WITH 9-CIS-RETINAL
 
Authors :  C. S. Bolze, R. E. Helbling, R. L. Owen, A. R. Pearson, G. Pompidor, F. Dwo M. R. Fuchs, J. Furrer, M. Golczak, K. Palczewski, M. Cascella, A. Stoc
Date :  18 Dec 13  (Deposition) - 08 Jan 14  (Release) - 22 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Retinaldehyde Binding Protein, Visual Cycle, 9-Cis-Retinal, Cellular Retinal Binding Protein, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. S. Bolze, R. E. Helbling, R. L. Owen, A. R. Pearson, G. Pompidor, F. Dworkowski, M. R. Fuchs, J. Furrer, M. Golczak, K. Palczewski, M. Cascella, A. Stocker
Human Cellular Retinaldehyde-Binding Protein Has Secondary Thermal 9-Cis-Retinal Isomerase Activity.
J. Am. Chem. Soc. V. 136 137 2014
PubMed-ID: 24328211  |  Reference-DOI: 10.1021/JA411366W

(-) Compounds

Molecule 1 - RETINALDEHYDE-BINDING PROTEIN 1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCELLULAR RETINALDEHYDE-BINDING PROTEIN, CELLULAR RETINALDEHYDE BINDING PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1RET1Ligand/IonRETINAL
2TLA1Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:204 , MET A:223 , PHE A:240 , VAL A:254BINDING SITE FOR RESIDUE RET A1307
2AC2SOFTWARELYS A:104 , ALA A:233 , ARG A:234 , LYS A:236 , LYS A:261 , ARG A:265BINDING SITE FOR RESIDUE TLA A1308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CIZ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:144 -Pro A:145

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_005140R151QRLBP1_HUMANDisease (RPA)28933989AR151Q
2UniProtVAR_037317M226KRLBP1_HUMANDisease (RPA)137853291AM226K
3UniProtVAR_015172R234WRLBP1_HUMANDisease (BRD)28933990AR234W

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CRAL_TRIOPS50191 CRAL-TRIO lipid binding domain profile.RLBP1_HUMAN136-297  1A:136-297

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 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_HUMAN5-47431A:23-4725
1.5ENST000002681255ENSE00000943553chr15:89760555-89760351205RLBP1_HUMAN48-116691A:48-11669
1.6ENST000002681256ENSE00000943554chr15:89758469-89758291179RLBP1_HUMAN116-175601A:116-17560
1.7ENST000002681257ENSE00000943555chr15:89755132-89754974159RLBP1_HUMAN176-228531A:176-22853
1.8ENST000002681258ENSE00000943556chr15:89754040-89753930111RLBP1_HUMAN229-265371A:229-26537
1.9ENST000002681259ENSE00000943557chr15:89753674-89753098577RLBP1_HUMAN266-317521A:266-30641

(-) Sequences/Alignments

Asymmetric/Biological Unit
   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:284
 aligned with RLBP1_HUMAN | P12271 from UniProtKB/Swiss-Prot  Length:317

    Alignment length:284
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302    
          RLBP1_HUMAN    23 EQLTTKDHGPVFGPCSQLPRHTLQKAKDELNEREETREEAVRELQEMVQAQAASGEELAVAVAERVQEKDSGFFLRFIRARKFNVGRAYELLRGYVNFRLQYPELFDSLSPEAVRCTIEAGYPGVLSSRDKYGRVVMLFNIENWQSQEITFDEILQAYCFILEKLLENEETQINGFCIIENFKGFTMQQAASLRTSDLRKMVDMLQDSFPARFKAIHFIHQPWYFTTTYNVVKPFLKSKLLERVFVHGDDLSGFYQEIDENILPSDFGGTLPKYDGKAVAEQLF 306
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....................hhhhhhhh......hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh...eeeeee.....eeeeee.........hhhhhhhhhhhhhhhhh.hhhhhhhheeeeee....hhhhhhh.hhhhhhhhhhhhh......eeeeeee....hhhhhhhhhh...hhhhhh.eeeee..........hhhhhhhhhh......hhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------Q--------------------------------------------------------------------------K-------W------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------CRAL_TRIO  PDB: A:136-297 UniProt: 136-297                                                                                                                        --------- PROSITE
           Transcript 1 (1) Exon 1.4  PDB: A:23-47   Exon 1.5  PDB: A:48-116 UniProt: 48-116                              -----------------------------------------------------------Exon 1.7  PDB: A:176-228 UniProt: 176-228            Exon 1.8  PDB: A:229-265             Exon 1.9  PDB: A:266-306 UniProt: 266-317 Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------Exon 1.6  PDB: A:116-175 UniProt: 116-175                   ----------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 4ciz A  23 EQLTTKDHGPVFGPCSQLPRHTLQKAKDELNEREETREEAVRELQEMVQAQAASGEELAVAVAERVQEKDSGFFLRFIRARKFNVGRAYELLRGYVNFRLQYPELFDSLSPEAVRCTIEAGYPGVLSSRDKYGRVVMLFNIENWQSQEITFDEILQAYCFILEKLLENEETQINGFCIIENFKGFTMQQAASLRTSDLRKMVDMLQDSFPARFKAIHFIHQPWYFTTTYNVVKPFLKSKLLERVFVHGDDLSGFYQEIDENILPSDFGGTLPKYDGKAVAEQLF 306
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302    

   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 4CIZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CIZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CIZ)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(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

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        RLBP1_HUMAN | P122711xgg 1xgh 3hx3 3hy5 4cj6

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