3CBS

CELLULAR RETINOIC ACID BINDING PROTEIN II IN COMPLEX WITH A SYNTHETIC RETINOIC ACID (RO-12 7310)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structures of cellular retinoic acid binding proteins I and II in complex with synthetic retinoids.

Chaudhuri, B.N.Kleywegt, G.J.Broutin-L'Hermite, I.Bergfors, T.Senn, H.Le Motte, P.Partouche, O.Jones, T.A.

(1999) Acta Crystallogr.,Sect.D 55: 1850-1857

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Retinoids play important roles in diverse cellular processes including growth, cell differentiation and vision. Many natural and synthetic retinoids are used as drugs in dermatology and oncology. A large amount of data has been accumulated on the cel ...

    Retinoids play important roles in diverse cellular processes including growth, cell differentiation and vision. Many natural and synthetic retinoids are used as drugs in dermatology and oncology. A large amount of data has been accumulated on the cellular activity of different synthetic retinoids. They are stabilized and transported inside the cell cytoplasm by binding and transport proteins, such as cellular retinol-binding proteins and cellular retinoic acid binding proteins (CRABPs). The structures of human CRABP II in complex with two different synthetic retinoids, Ro13-6307 and Ro12--7310 (at 2.1 and 2.0 A resolution, respectively) and of bovine CRABP I in complex with a retinobenzoic acid, Am80 (at 2.8 A resolution) are described. The binding affinities of human CRABP I and II for the retinoids studied here have been determined. All these compounds have comparable binding affinities (nanomolar range) for both CRABPs. Apart from the particular interactions of the carboxylate group of the retinoids with specific protein groups, each structure reveals characteristic interactions. Studying the atomic details of the interaction of retinoids with retinoid-binding proteins facilitates the understanding of the kinetics of retinoid trafficking inside the cytoplasm.


    Related Citations: 
    • Crystal Structure 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
    • Crystallisation and Preliminary X-Ray Analysis of Recombinant Bovine Cellular Retinoic Acid-Binding Protein
      Bergfors, T.,Kleywegt, G.J.,Jones, T.A.
      (1994) Acta Crystallogr.,Sect.D 50: 370
    • Lipid-Binding Proteins: A Family of Fatty Acid and Retinoid Transport Proteins
      Banaszak, L.,Winter, N.,Xu, Z.,Bernlohr, D.A.,Cowan, S.W.,Jones, T.A.
      (1994) Adv.Protein Chem. 45: 89


    Organizational Affiliation

    Department of Cell Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24, Uppsala, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (CRABP-II)
A
137Homo sapiensMutation(s): 0 
Gene Names: CRABP2
Find proteins for P29373 (Homo sapiens)
Go to Gene View: CRABP2
Go to UniProtKB:  P29373
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R12
Query on R12

Download SDF File 
Download CCD File 
A
(2E,4E,6E,8E)-9-(4-hydroxy-2,3,6-trimethylphenyl)-3,7-dimethylnona-2,4,6,8-tetraenoic acid
C20 H24 O3
CAAFTBWHFUPDGX-OFCLTBKTSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
R12Ki: 58 nM BINDINGMOAD
R12IC50: 58 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 38.030α = 90.00
b = 48.320β = 90.00
c = 83.820γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-12-22
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-11-02
    Type: Non-polymer description