1ERB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The interaction of N-ethyl retinamide with plasma retinol-binding protein (RBP) and the crystal structure of the retinoid-RBP complex at 1.9-A resolution.

Zanotti, G.Malpeli, G.Berni, R.

(1993) J Biol Chem 268: 24873-24879

  • DOI: 10.2210/pdb1erb/pdb
  • Primary Citation of Related Structures:  
    1ERB

  • PubMed Abstract: 
  • The three-dimensional structure of bovine plasma retinol-binding protein (RBP) complexed with N-ethyl retinamide has been determined at 1.9-A resolution. The crystals of the complex (space group P2(1)2(1)2(1), a = 46.27, b = 49.11, c = 76.41 A) are isomorphous with those of bovine holo and apoRBP ...

    The three-dimensional structure of bovine plasma retinol-binding protein (RBP) complexed with N-ethyl retinamide has been determined at 1.9-A resolution. The crystals of the complex (space group P2(1)2(1)2(1), a = 46.27, b = 49.11, c = 76.41 A) are isomorphous with those of bovine holo and apoRBP. The final crystallographic R factor is 0.172 for 11,261 observed reflections. The model of the retinoid-RBP complex is nearly identical to that of bovine retinol-RBP complex; the root mean square deviations between the alpha-carbons in the two proteins is 0.15 A. The N-ethyl retinamide molecule fits in the beta-barrel in the same position previously occupied by the vitamin. The ethyl group of the retinoid replaces the retinol hydroxyl group and a water molecule hydrogen bonded to it. This substitution has no consequence on the overall conformation of the protein. The modification of the functional end group of retinol does not lead to an apparent loss of affinity of the retinol analog for apoRBP, as established by means of fluorometric titrations with N-ethyl retinamide. However, the binding of the retinoid to RBP abolishes or greatly reduces the affinity of RBP for transthyretin. This behavior further supports the hypothesis that the area of the entrance of the beta-barrel, which includes the ethyl group of the retinoid bound to RBP, is involved in the interaction with transthyretin. Moreover, it indicates a high degree of complementarity of interacting surfaces between RBP and transthyretin. In fact, the replacement of the retinol hydroxyl group and quite small structural changes in the above region of the RBP molecule drastically affect the protein-protein recognition.


    Related Citations: 
    • 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
    • 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
    • The Bovine Plasma Retinol-Binding Protein. Amino Acid Sequence, Interaction with Transthyretin, Crystallization and Preliminary X-Ray Data
      Berni, R., Stoppini, M., Zapponi, C.M., Meloni, M.L., Monaco, H.L., Zanotti, G.
      (1990) Eur J Biochem 192: 507

    Organizational Affiliation

    Department of Organic Chemistry, University of Padova, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RETINOL BINDING PROTEINA183Bos taurusMutation(s): 0 
Gene Names: RBP4
UniProt
Find proteins for P18902 (Bos taurus)
Explore P18902 
Go to UniProtKB:  P18902
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18902
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ETR
Query on ETR

Download Ideal Coordinates CCD File 
B [auth A]N-ETHYL RETINAMIDE
C22 H33 N O
WKYDOCGICAMTKE-NBIQJRODSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
ETR Binding MOAD:  1ERB Kd: 8 (nM) from 1 assay(s)
PDBBind:  1ERB Kd: 8 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.27α = 90
b = 49.11β = 90
c = 76.41γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 1993-10-01 
  • Released Date: 1994-01-31 
  • Deposition Author(s): Zanotti, G., Berni, R.

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other