1KT5

Crystal structure of bovine holo-RBP at pH 4.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

High-resolution Structures of Retinol-binding Protein in Complex with Retinol: pH-induced Protein Structural Changes in the Crystal State

Calderone, V.Berni, R.Zanotti, G.

(2003) J Mol Biol 329: 841-850

  • DOI: 10.1016/s0022-2836(03)00468-6
  • Primary Citation of Related Structures:  
    1KT7, 1KT6, 1KT5, 1KT4, 1KT3

  • PubMed Abstract: 
  • The targeted delivery of non-polar ligands by binding proteins to membranes or membrane receptors involves the release of these ligands on or near the plasma membrane of target cells. Because these hydrophobic ligands are often bound inside a deep cavity of binding proteins, as shown previously for plasma retinol-binding protein (RBP), their release from these proteins might require the destabilization of the protein structure by partially denaturing conditions, such as those possibly present near plasma membranes ...

    The targeted delivery of non-polar ligands by binding proteins to membranes or membrane receptors involves the release of these ligands on or near the plasma membrane of target cells. Because these hydrophobic ligands are often bound inside a deep cavity of binding proteins, as shown previously for plasma retinol-binding protein (RBP), their release from these proteins might require the destabilization of the protein structure by partially denaturing conditions, such as those possibly present near plasma membranes. RBP is a plasma transport protein which delivers specifically retinol from its store sites to target cells. Here, we report the high-resolution (1.1-1.4A) crystal structures of bovine holo-RBP at five different pH values, ranging from 9 to 2. While unraveling details of the native protein structure and of the interactions with retinol at nearly atomic resolution at neutral pH, this study provides evidence for definite pH-induced modifications of several structural features of RBP. The structure most representative of the changes that holo-RBP undergoes at different pH values is that of its flexible state at pH 2. At this pH, most significant are the alteration of the arrangement of salt bridges and of the network of water molecules/H-bonds that participates in the retinol-RBP interaction, an appreciable increase of the volume of the beta-barrel cavity, a considerably higher degree of mobility of the RBP-bound ligand and of several protein regions and the disorder of a large number of solvent molecules that are ordered at neutral pH. These changes are likely to be accompanied by a modification of the pattern of charge distribution on the protein surface. All these changes, which reveal a substantially lowered conformational stability of RBP, presumably occur at the initial stages of the acidic denaturation of RBP and are possibly associated with a facilitated release of the retinol molecule from its carrier protein.


    Related Citations: 
    • Crystallographic Refinement of Human Serum Retinol Binding Protein at 2A Resolution.
      Cowan, S.W., Newcomer, M.E., Jones, T.A.
      (1990) Proteins 8: 44
    • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Plasma retinol-binding proteinA175Bos taurusMutation(s): 0 
Gene Names: RBP4
UniProt
Find proteins for P18902 (Bos taurus)
Explore P18902 
Go to UniProtKB:  P18902
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RTL
Query on RTL

Download Ideal Coordinates CCD File 
B [auth A]RETINOL
C20 H30 O
FPIPGXGPPPQFEQ-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.293α = 90
b = 48.769β = 90
c = 74.613γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
SHELXmodel building
SHELXL-97refinement
CCP4data scaling
SHELXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-06-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance