1HBP

CRYSTAL STRUCTURE OF LIGANDED AND UNLIGANDED FORMS OF BOVINE PLASMA RETINOL-BINDING PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 10728-10738

  • Primary Citation of Related Structures:  1HBQ

  • PubMed Abstract: 
  • The three-dimensional structures of bovine plasma retinol-binding protein (bRBP) complexed with retinol (space group P2(1)2(1)2(1), a = 46.08, b = 49.12, c = 76.10 A) and of the unliganded protein prepared in vitro by extracting retinol with ethyl et ...

    The three-dimensional structures of bovine plasma retinol-binding protein (bRBP) complexed with retinol (space group P2(1)2(1)2(1), a = 46.08, b = 49.12, c = 76.10 A) and of the unliganded protein prepared in vitro by extracting retinol with ethyl ether (space group P2(1)2(1)2(1), a = 46.55, b = 48.97, c = 76.87 A) have been solved at 1.9 and 1.7 A resolution, respectively. The final crystallographic R factors are 0.190 for holobRBP and 0.196 for the unliganded bRBP. The model for the bovine holoprotein is quite similar to that of the human protein, with which it exhibits 92% sequence similarity. The root mean square deviation between the alpha-carbons in the two proteins is 0.31 A. The retinol binding site is almost completely preserved. The loops that surround the opening of the beta-barrel are also particularly conserved, in contrast with the presence of several substitutions in parts of the RBP molecule opposite the opening of the calyx that binds retinol. Despite the fact that unliganded bovine RBP was prepared and crystallized using procedures completely different from those used to obtain the unliganded human RBP, the conformational differences between unliganded and liganded forms of bRBP are almost identical to those found previously between the same forms of human RBP. They mainly involve a few residues in the region extending from amino acid residues 32 to 37. Therefore, similar differences are very likely to exist between holoRBP and the physiologically occurring apoprotein. A not yet identified electron density, different in shape and orientation from retinol, also occupies the central cavity of the beta-barrel in the unliganded bRBP, as found for unliganded human RBP. The functional consequences of the conformational change induced by the removal of retinol on the interaction between RBP and transthyretin, coupled with the conservation of the entrance loops of the beta-barrel in mammalian RBPs, are consistent with their participation in molecular interactions.


    Related Citations: 
    • 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
    • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RETINOL BINDING PROTEIN
A
183Bos taurusGene Names: RBP4
Find proteins for P18902 (Bos taurus)
Go to Gene View: RBP4
Go to UniProtKB:  P18902
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RTL
Query on RTL

Download SDF File 
Download CCD File 
A
RETINOL
C20 H30 O
FPIPGXGPPPQFEQ-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Work: 0.190 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.080α = 90.00
b = 49.120β = 90.00
c = 76.100γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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