1LPJ

Human cRBP IV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Ligand binding and structural analysis of a human putative cellular retinol-binding protein

Folli, C.Calderone, V.Ramazzina, I.Zanotti, G.Berni, R.

(2002) J Biol Chem 277: 41970-41977

  • DOI: 10.1074/jbc.M207124200
  • Primary Citation of Related Structures:  
    1LPJ

  • PubMed Abstract: 
  • Three cellular retinol-binding protein (CRBP) types (CRBP I, II, and III) with distinct tissue distributions and retinoid binding properties have been structurally characterized thus far. A human binding protein, whose mRNA is expressed primarily in kidney, heart, and transverse colon, is shown here to be a CRBP family member (human CRBP IV), according to amino acid sequence, phylogenetic analysis, gene structure organization, and x-ray structural analysis ...

    Three cellular retinol-binding protein (CRBP) types (CRBP I, II, and III) with distinct tissue distributions and retinoid binding properties have been structurally characterized thus far. A human binding protein, whose mRNA is expressed primarily in kidney, heart, and transverse colon, is shown here to be a CRBP family member (human CRBP IV), according to amino acid sequence, phylogenetic analysis, gene structure organization, and x-ray structural analysis. Retinol binding to CRBP IV leads to an absorption spectrum distinct from a typical holo-CRBP spectrum and is characterized by an affinity (K(d) = approximately 200 nm) lower than those for CRBP I, II, and III, as established in direct and competitive binding assays. As revealed by mutagenic analysis, the presence in CRBP IV of His(108) in place of Gln(108) is not responsible for the unusual holo-CRBP IV spectrum. The 2-A resolution crystal structure of human apo-CRBP IV is very similar to those of other structurally characterized CRBPs. The side chain of Tyr(60) is present within the binding cavity of the apoprotein and might affect the interaction with the retinol molecule. These results indicate that human CRBP IV belongs to a clearly distinct CRBP subfamily and suggest a relatively different mode of retinol binding for this binding protein.


    Related Citations: 
    • 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
    • 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
    • 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 U S A 98: 3710

    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, University of Parma, Italy.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Retinol-binding protein IV, cellularA133Homo sapiensMutation(s): 0 
Gene Names: RBP7
UniProt & NIH Common Fund Data Resources
Find proteins for Q96R05 (Homo sapiens)
Explore Q96R05 
Go to UniProtKB:  Q96R05
PHAROS:  Q96R05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96R05
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.053α = 90
b = 57.186β = 104.03
c = 67.939γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance