1XCA

APO-CELLULAR RETINOIC ACID BINDING PROTEIN II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of apo-cellular retinoic acid-binding protein type II (R111M) suggests a mechanism of ligand entry.

Chen, X.Tordova, M.Gilliland, G.L.Wang, L.Li, Y.Yan, H.Ji, X.

(1998) J Mol Biol 278: 641-653

  • DOI: 10.1006/jmbi.1998.1734
  • Primary Citation of Related Structures:  
    1XCA

  • PubMed Abstract: 
  • The crystal structure of unliganded mutant R111M of human cellular retinoic acid-binding protein type II (apo-CRABPII (R111M)) has been determined at 2.3 A and refined to a crystallographic R-factor of 0. 18. Although the mutant protein has lower aff ...

    The crystal structure of unliganded mutant R111M of human cellular retinoic acid-binding protein type II (apo-CRABPII (R111M)) has been determined at 2.3 A and refined to a crystallographic R-factor of 0. 18. Although the mutant protein has lower affinity for all-trans-retinoic acid (RA) than the wild-type, it is properly folded, and its conformation is very similar to the wild-type. apo-CRABPII (R111M) crystallizes in space group P1 with two molecules in the unit cell. The two molecules have high structural similarity except that their alpha2 helices differ strikingly. Analyses of the molecular conformation and crystal packing environment suggest that one of the two molecules assumes a conformation compatible with RA entry. Three structural elements encompassing the opening of the binding pocket exhibit large conformational changes, when compared with holo-CRABPII, which include the alpha2 helix and the betaC-betaD and betaE-betaF hairpin loops. The alpha2 helix is unwound at its N terminus, which appears to be essential for the opening of the RA-binding pocket. Three arginine side-chains (29, 59, and 132) are found with their guanidino groups pointing into the RA-binding pocket. A three-step mechanism of RA entry has been proposed, addressing the opening of the RA entrance, the electrostatic potential that directs entry of RA into the binding pocket, and the intramolecular interactions that stabilize the RA.CRABPII complex via locking the three flexible structural elements when RA is bound.


    Related Citations: 
    • Crystal Structure of Cellular Retinoic Acid Binding Protein I Shows Increased Access to the Binding Cavity due to Formation of an Intermolecular Beta-Sheet
      Thompson, J.R., Bratt, J.M., Banaszak, L.J.
      (1995) J Mol Biol 252: 433
    • Crystal Structures of Cellular Retinoic Acid Binding Proteins I and II in Complex with All-Trans-Retinoic Acid and a Synthetic Retinoid
      Kleywegt, G.J., Bergfors, T., Senn, H., Le Motte, P., Gsell, B., Shudo, K., Jones, T.A.
      (1994) Structure 2: 1241

    Organizational Affiliation

    ABL-Basic Research Program, National Cancer Institute-Frederick Cancer Research and Development Center, Frederick, MD 21702, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELLULAR RETINOIC ACID BINDING PROTEIN TYPE IIAB137Homo sapiensMutation(s): 1 
Gene Names: CRABP2
Find proteins for P29373 (Homo sapiens)
Explore P29373 
Go to UniProtKB:  P29373
NIH Common Fund Data Resources
PHAROS  P29373
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.58α = 106.41
b = 62.27β = 90.69
c = 35.12γ = 110.64
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1996-12-31 
  • Released Date: 1998-07-01 
  • Deposition Author(s): Chen, X., Ji, X.

Revision History 

  • Version 1.0: 1998-07-01
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-12-11
    Changes: Advisory, Derived calculations, Other