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(-) Description

Title :  CHICKEN PLASMA RETINOL-BINDING PROTEIN (RBP)
 
Authors :  G. Zanotti, V. Calderone, R. Berni
Date :  24 Apr 01  (Deposition) - 16 Jan 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Rbp, Retinol, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Zanotti, V. Calderone, M. Beda, G. Malpeli, C. Folli, R. Berni
Structure Of Chicken Plasma Retinol-Binding Protein
Biochim. Biophys. Acta V. 1550 64 2001
PubMed-ID: 11738088  |  Reference-DOI: 10.1016/S0167-4838(01)00268-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLASMA RETINOL-BINDING PROTEIN
    ChainsA
    Organism CommonCHICKEN
    Organism ScientificGALLUS GALLUS
    Organism Taxid9031
    SynonymPRBP

 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
1CD1Ligand/IonCADMIUM ION
2RTL1Ligand/IonRETINOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:33 , ASP A:140 , LYS A:142 , HOH A:260BINDING SITE FOR RESIDUE CD A 177
2AC2SOFTWARELEU A:35 , PHE A:36 , MET A:88 , LEU A:97 , GLN A:98BINDING SITE FOR RESIDUE RTL A 176

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:4 -A:160
2A:70 -A:174
3A:120 -A:129

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1IIU)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPOCALINPS00213 Lipocalin signature.RET4_CHICK35-48  1A:14-27

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSGALT000000107081ENSGALE00000262824chr6:21493042-2149306221RET4_CHICK-00--
1.2bENSGALT000000107082bENSGALE00000071060chr6:21493232-21493358127RET4_CHICK1-40401A:2-1918
1.3ENSGALT000000107083ENSGALE00000071059chr6:21493970-21494106137RET4_CHICK41-86461A:20-6546
1.4ENSGALT000000107084ENSGALE00000071061chr6:21494264-21494370107RET4_CHICK86-122371A:65-10137
1.5ENSGALT000000107085ENSGALE00000071058chr6:21495784-21495996213RET4_CHICK122-193721A:101-17272
1.6aENSGALT000000107086aENSGALE00000262689chr6:21498012-21498204193RET4_CHICK193-19641A:172-1754

(-) 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:174
 aligned with RET4_CHICK | P41263 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:174
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192    
           RET4_CHICK    23 RDCRVSSFKVKENFDKNRYSGTWYAMAKKDPEGLFLQDNVVAQFTVDENGQMSATAKGRVRLFNNWDVCADMIGSFTDTEDPAKFKMKYWGVASFLQKGNDDHWVVDTDYDTYALHYSCRELNEDGTCADSYSFVFSRDPKGLPPEAQKIVRQRQIDLCLDRKYRVIVHNGFCS 196
               SCOP domains d1iiua_ A: Retinol binding protein                                                                                                                                             SCOP domains
               CATH domains 1iiuA00 A:2-175  [code=2.40.128.20, no name defined]                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhh......hhhhhheeeeeeeee........eeeeeeeee.....eeeeeeeeee.....eeeeeeeeeee......eeeeeeee.......eeeeeeeeee....eeeeeeeeee.....eeeeeeeeee......hhhhhhhhhhhhhh.......ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------LIPOCALIN     ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b         Exon 1.3  PDB: A:20-65 UniProt: 41-86         -----------------------------------Exon 1.5  PDB: A:101-172 UniProt: 122-193                               --- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------Exon 1.4  PDB: A:65-101              ----------------------------------------------------------------------1.6a Transcript 1 (2)
                 1iiu A   2 MDCRVSSFKVKENFDKNRYSGTWYAMAKKDPEGLFLQDNVVAQFTVDENGQMSATAKGRVRLFNNWDVCADMIGSFTDTEDPAKFKMKYWGVASFLQKGNDDHWVVDTDYDTYALHYSCRELNEDGTCADSYSFVFSRDPKGLPPEAQKIVRQRQIDLCLDRKYRVIVHNGFCS 175
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171    

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RET4_CHICK | P41263)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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:0005501    retinoid binding    Interacting selectively and non-covalently with 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: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:0034632    retinol transporter activity    Enables the directed movement of retinol into, out of or within a cell, or between cells. Retinol is 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.
    GO:0036094    small molecule binding    Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
    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:0001654    eye development    The process whose specific outcome is the progression of the eye over time, from its formation to the mature structure. The eye is the organ of sight.
    GO:0006094    gluconeogenesis    The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
    GO:0042593    glucose homeostasis    Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
    GO:0030277    maintenance of gastrointestinal epithelium    Protection of epithelial surfaces of the gastrointestinal tract from proteolytic and caustic digestive agents.
    GO:0001555    oocyte growth    The developmental growth process in which an oocyte irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0032024    positive regulation of insulin secretion    Any process that activates or increases the frequency, rate or extent of the regulated release of insulin.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0043627    response to estrogen    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 stimulus by an estrogen, C18 steroid hormones that can stimulate the development of female sexual characteristics.
    GO:0032526    response to retinoic acid    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 retinoic acid stimulus.
    GO:0009615    response to virus    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 from a virus.
    GO:0033189    response to vitamin A    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 vitamin A stimulus.
    GO:0042572    retinol metabolic process    The chemical reactions and pathways involving retinol, one of the three compounds that makes up vitamin A.
    GO:0034633    retinol transport    The directed movement of retinol into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Retinol is 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.
    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.
cellular component
    GO:0030136    clathrin-coated vesicle    A vesicle with a coat formed of clathrin connected to the membrane via one of the clathrin adaptor complexes.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0060417    yolk    The cytoplasmic part that serves as a nutrient reserve or energy source for the developing embryo.
    GO:0060418    yolk plasma    Discrete structures that partition the water-soluble portion of the yolk of oocytes and ova, which may or may not be membrane enclosed.

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(-) Related Entries Specified in the PDB File

1aqb 1hbp 1hbq 1rbp