2FS7

Crystal Structure of Apo-Cellular Retinoic Acid Binding Protein Type II At 1.55 Angstroms Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.144 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structure of Apo-wild-type cellular retinoic acid binding protein II at 1.4 A and its relationship to ligand binding and nuclear translocation.

Vaezeslami, S.Mathes, E.Vasileiou, C.Borhan, B.Geiger, J.H.

(2006) J.Mol.Biol. 363: 687-701

  • DOI: 10.1016/j.jmb.2006.08.059
  • Primary Citation of Related Structures:  2FR3, 2FRS, 2FS6

  • PubMed Abstract: 
  • CRABPII is a small, cytosolic protein that solubilizes and transfers retinoic acid (RA) to the nucleus while also enhancing its transcriptional activity. We have determined the first high-resolution structure of apo-wild type (WT) CRABPII at 1.35 A. ...

    CRABPII is a small, cytosolic protein that solubilizes and transfers retinoic acid (RA) to the nucleus while also enhancing its transcriptional activity. We have determined the first high-resolution structure of apo-wild type (WT) CRABPII at 1.35 A. Using three different data sets collected on apo-WT CRABPII we have shown that apo- and holo-CRABPII share very similar structures. Binding of RA appears to increase the overall rigidity of the structure, although the induced structural changes are not as pronounced as previously thought. The enhanced structural rigidity may be an important determinant for the enhanced nuclear localization of the RA-bound protein. Comparison of our apo-WT with a mutant apo-CRABPII structure shows that mutation of Arg111, a conserved residue of CRABPII and a key residue in RA binding, causes structural changes in the molecule. We further investigated the structural importance of conserved residues by determining the structure of the F15W mutant CRABPII (F15W-CRABPII). Our structures also demonstrate structural changes induced by crystal packing and show that a crystal can harbor demonstrative structural differences in the asymmetric unit.


    Related Citations: 
    • Determining crystal structures of proteins and protein complexes by x-ray crystallography: x-ray crystallographic studies of the mutants of cellular retinoic acid binding protein type ii toward designing a mimic of rhodopsin
      Vaezeslami, S.
      () Thesis --: --


    Organizational Affiliation

    Chemistry Department, Michigan State University, East Lansing, MI 48824-1322, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cellular retinoic acid-binding protein 2
A, B
137Homo sapiensGene Names: CRABP2
Find proteins for P29373 (Homo sapiens)
Go to Gene View: CRABP2
Go to UniProtKB:  P29373
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.144 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 34.475α = 73.09
b = 37.220β = 75.74
c = 57.597γ = 87.22
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-19
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Advisory, Refinement description