1KT6

Crystal structure of bovine holo-RBP at pH 9.0


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.1 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.188 

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

  • Primary Citation of Related Structures:  1KT3, 1KT4, 1KT5, 1KT7

  • 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 ca ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
plasma 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: 1.1 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 46.861α = 90.00
b = 48.948β = 90.00
c = 75.654γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SHELXmodel building
SHELXphasing
CCP4data scaling
SCALAdata scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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