1FEL

CRYSTALLOGRAPHIC STUDIES ON COMPLEXES BETWEEN RETINOIDS AND PLASMA RETINOL-BINDING PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystallographic studies on complexes between retinoids and plasma retinol-binding protein.

Zanotti, G.Marcello, M.Malpeli, G.Folli, C.Sartori, G.Berni, R.

(1994) J Biol Chem 269: 29613-29620

  • Primary Citation of Related Structures:  
    1FEN, 1FEM, 1FEL

  • PubMed Abstract: 
  • The three-dimensional structures of complexes between bovine plasma retinol-binding protein (RBP) and three retinol analogs with different end groups (fenretinide, all-trans retinoic acid, and axerophthene) have been determined to 1.8-1.9-A resolutio ...

    The three-dimensional structures of complexes between bovine plasma retinol-binding protein (RBP) and three retinol analogs with different end groups (fenretinide, all-trans retinoic acid, and axerophthene) have been determined to 1.8-1.9-A resolution. Their models are very similar to that of the bovine retinol.RBP complex: the root mean square deviations between equivalent alpha-carbons in the two proteins range from 0.17 to 0.24 A. The retinoid molecules fit in the beta-barrel cavity assuming the same conformation of the vitamin, and the substitutions have no consequences on the overall protein structure. While confirming that an intact hydroxyl end group is not an absolute requirement for a correct retinoid binding to RBP, this study has shown the occurrence of conformational changes, although limited, in the rather flexible loop region at the entrance of the beta-barrel upon fenretinide and retinoic acid binding. These changes are suitable for accommodating the end groups of the above retinoids. Instead, no such changes have been revealed in RBP complexed with axerophthene, a retinol analog bearing a hydrogen atom in place of the hydroxyl end group. The protein conformational changes in the above loop region, the steric hindrance of bulky end groups of bound retinoids, and the lack of the retinol hydroxyl group appear to be responsible for the possible reduced affinity of retinoids for RBP relative to retinol and, at the same time, for the abolished or reduced affinity of retinoid.RBP complexes for transthyretin relative to retinol-RBP.


    Related Citations: 
    • The Interaction of N-Ethyl Retinamide with Plasma Retinol-Binding Protein (Rbp) and the Crystal Structure of the Retinoid-Rbp Complex at 1.9 Angstroms Resolution
      Zanotti, G., Malpeli, G., Berni, R.
      (1993) J Biol Chem 268: 24873
    • Crystal Structure of Liganded and Unliganded Forms of Bovine Plasma Retinol-Binding Protein
      Zanotti, G., Berni, R., Monaco, H.L.
      (1993) J Biol Chem 268: 10728
    • Crystal Structure of the Trigonal Form of Human Plasma Retinol-Binding Protein at 2.5 Angstroms Resolution
      Zanotti, G., Ottonello, S., Berni, R., Monaco, H.L.
      (1993) J Mol Biol 230: 613

    Organizational Affiliation

    Department of Organic Chemistry, University of Padova, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RETINOL BINDING PROTEINA183Bos taurusMutation(s): 0 
Gene Names: RBP4
Find proteins for P18902 (Bos taurus)
Explore P18902 
Go to UniProtKB:  P18902
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FEN
Query on FEN

Download CCD File 
A
N-(4-HYDROXYPHENYL)ALL-TRANS RETINAMIDE
C26 H33 N O2
AKJHMTWEGVYYSE-FXILSDISSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FENEC50:  2372   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.63α = 90
b = 49.26β = 90
c = 76.63γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-11-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance