1KQX

Crystal structure of apo-CRBP from zebrafish


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Identification and structural analysis of a zebrafish apo and holo cellular retinol-binding protein.

Calderone, V.Folli, C.Marchesani, A.Berni, R.Zanotti, G.

(2002) J.Mol.Biol. 321: 527-535

  • Primary Citation of Related Structures:  1KQW

  • PubMed Abstract: 
  • Cellular retinol-binding proteins (CRBPs) are cytoplasmic retinol-specific binding proteins. Mammalian CRBPs have been thoroughly characterised previously. Here we report on the identification and X-ray structural analysis of the apo (1.7A resolution ...

    Cellular retinol-binding proteins (CRBPs) are cytoplasmic retinol-specific binding proteins. Mammalian CRBPs have been thoroughly characterised previously. Here we report on the identification and X-ray structural analysis of the apo (1.7A resolution) and holo (1.4A resolution) forms of a zebrafish CRBP. According to amino acid sequence and structure analyses, the zebrafish CRBP that we have identified resembles closely mammalian CRBP II, suggesting that it is the zebrafish orthologue of this mammalian CRBP type. Zebrafish CRBP forms a tight complex with all-trans retinol, producing an absorption spectrum similar to those of mammalian holo-CRBPs, albeit slightly blue-shifted. The superposition of the alpha-carbon atoms of the liganded (complexed with retinol) and unliganded forms of zebrafish CRBP shows significant differences in correspondence of the betaC-betaD (residues 55-58) and betaE-betaF (residues 74-77) turns, providing evidence for the occurrence of conformational changes accompanying retinol binding/release. Remarkable and well-defined ligand-dependent conformational changes in the protein region comprising the two beta-turns affect both the main chain and the side-chains of several residues. The two beta-turns project towards the interior of the cavity devoid of ligand of the apoprotein. The side-chains of F57, Y60 and L77 change substantially their orientation and position in the apoprotein relative to the holoprotein. In the beta-barrel internal cavity of apo-CRBP they occupy some of the space that is otherwise occupied by bound retinol in holo-CRBP, and are displaced from these positions on ligand binding. These results indicate that a flexible area encompassing the betaC-betaD and betaE-betaF turns may serve as the ligand portal and that these turns undergo conformational changes associated with the not yet clarified mechanism of retinol binding and release in CRBPs.


    Related Citations: 
    • Identification, retinoid binding and X-ray analysis of a human retinol-binding protein
      Folli, C.,Calderone, V.,Ottonello, S.,Bolchi, A.,Zanotti, G.,Stoppini, M.,Berni, R.
      (2001) Proc.Natl.Acad.Sci.USA 98: 3710
    • Crystal structures of holo and apo-cellular retinol-binding protein II
      Winter, N.S.,Bratt, J.M.,Banaszak, L.J.
      (1993) J.Mol.Biol. 230: 1247
    • Crystallographic Studies on a Family of Cellular Lipophilic Transport Proteins. Refinement of P2 Myelin Protein and the Structure Determination and Refinement of Cellular Retinol-binding Protein in Complex with All-trans-retinol
      Cowan, S.W.,Newcomer, M.E.,Jones, T.A.
      (1993) J.Mol.Biol. 230: 1225


    Organizational Affiliation

    Department of Organic Chemistry, University of Padova, and Biopolymer Research Center, Italian National Research Council, Via Marzolo 1, 35131, Padova, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cellular retinol-binding protein
A
134Danio rerioGene Names: rbp2a (rbp2)
Find proteins for Q8UVG6 (Danio rerio)
Go to UniProtKB:  Q8UVG6
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.195 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 88.759α = 90.00
b = 88.759β = 90.00
c = 38.437γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling
SHELXmodel building
SHELXL-97refinement
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-08-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance