Crystal structure of holo-CRBP from zebrafish

Experimental Data Snapshot

  • Resolution: 1.38 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.165 

Starting Model: experimental
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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

  • DOI: https://doi.org/10.1016/s0022-2836(02)00628-9
  • Primary Citation of Related Structures:  
    1KQW, 1KQX

  • 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) 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.

  • Organizational Affiliation

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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular retinol-binding protein134Danio rerioMutation(s): 0 
Find proteins for Q8UVG6 (Danio rerio)
Explore Q8UVG6 
Go to UniProtKB:  Q8UVG6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8UVG6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on RTL

Download Ideal Coordinates CCD File 
C20 H30 O
Experimental Data & Validation

Experimental Data

  • Resolution: 1.38 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.165 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.018α = 90
b = 89.018β = 90
c = 38.271γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description