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(-) Description

Title :  THE CRYSTAL STRUCTURES OF HOLO-AND APO-CELLULAR RETINOL BINDING PROTEIN II
 
Authors :  N. Winter, L. Banaszak
Date :  09 Dec 92  (Deposition) - 31 Oct 93  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Retinol Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. S. Winter, J. M. Bratt, L. J. Banaszak
Crystal Structures Of Holo And Apo-Cellular Retinol-Binding Protein Ii.
J. Mol. Biol. V. 230 1247 1993
PubMed-ID: 8487303  |  Reference-DOI: 10.1006/JMBI.1993.1239
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CELLULAR RETINOL BINDING PROTEIN II
    Chains: A, B
    Engineered: YES
    Organism Common: BLACK RAT
    Organism Scientific: RATTUS RATTUS
    Organism Taxid: 10117

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1OPA)

(-) Sites  (0, 0)

(no "Site" information available for 1OPA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FABPPS00214 Cytosolic fatty-acid binding proteins signature.RET2_RAT7-24
 		  2A:6-23
B:6-23

(-) Exons   (4, 8)

Asymmetric/Biological Unit (4, 8)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000187551ENSRNOE00000132835chr8:103665461-103665588128RET2_RAT1-25252A:1-24
B:1-24		24
24
1.2ENSRNOT000000187552ENSRNOE00000213037chr8:103673980-103674158179RET2_RAT25-84602A:24-83
B:24-83		60
60
1.3ENSRNOT000000187553ENSRNOE00000133487chr8:103683992-103684093102RET2_RAT85-118342A:84-117
B:84-117		34
34
1.4ENSRNOT000000187554ENSRNOE00000213019chr8:103685522-103685768247RET2_RAT119-134162A:118-133
B:118-133		16
16

(-) 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:133
 aligned with RET2_RAT | P06768 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   
             RET2_RAT     2 TKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK 134
               SCOP domains d1opaa_ A: Cellular retinol-binding protein II (CRBP)                                                                                 SCOP domains
               CATH domains 1opaA00 A:1-133  [code=2.40.128.20, no name defined]                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeee.hhhhhhhh...hhhhhhhh.eeeeeeeeee..eeeeeeeee.eeeeeeeee.eeeeeeee....eeeeeeeee...eeeeeee..eeeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----FABP  PDB: A:6-23 -------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:1-24   -----------------------------------------------------------Exon 1.3  PDB: A:84-117           Exon 1.4         Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.2  PDB: A:24-83 UniProt: 25-84                       -------------------------------------------------- Transcript 1 (2)
                 1opa A   1 TKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130   


Chain B from PDB  Type:PROTEIN  Length:133
 aligned with RET2_RAT | P06768 from UniProtKB/Swiss-Prot  Length:134

    Alignment length:133
                                    11        21        31        41        51        61        71        81        91       101       111       121       131   
             RET2_RAT     2 TKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK 134
               SCOP domains d1opab_ B: Cellular retinol-binding protein II (CRBP)                                                                                 SCOP domains
               CATH domains 1opaB00 B:1-133  [code=2.40.128.20, no name defined]                                                                                  CATH domains
           Pfam domains (1) ----Lipocalin-1opaB01 B:5-133                                                                                                         Pfam domains (1)
           Pfam domains (2) ----Lipocalin-1opaB02 B:5-133                                                                                                         Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeeee.hhhhhhhh...hhhhhhhh.eeeeeeeeee..eeeeeeeee.eeeeeeeee.eeeeeeee....eeeeeeeee...eeeeeee..eeeeeeeeeee..eeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----FABP  PDB: B:6-23 -------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:1-24   -----------------------------------------------------------Exon 1.3  PDB: B:84-117           Exon 1.4         Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.2  PDB: B:24-83 UniProt: 25-84                       -------------------------------------------------- Transcript 1 (2)
                 1opa B   1 TKDQNGTWEMESNENFEGYMKALDIDFATRKIAVRLTQTKIIVQDGDNFKTKTNSTFRNYDLDFTVGVEFDEHTKGLDGRNVKTLVTWEGNTLVCVQKGEKENRGWKQWVEGDKLYLELTCGDQVCRQVFKKK 133
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Calycin (163)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (RET2_RAT | P06768)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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:0042572    retinol metabolic process    The chemical reactions and pathways involving retinol, one of the three compounds 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.
    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: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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RET2_RAT | P06768: 1b4m 1eii 1opb

(-) Related Entries Specified in the PDB File

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