5OGB

Human Cellular Retinoic Acid Binding Protein II (CRABPII) with bound synthetic retinoid DC360.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Fluorescent Retinoic Acid Analogues as Probes for Biochemical and Intracellular Characterization of Retinoid Signaling Pathways.

Chisholm, D.R.Tomlinson, C.W.E.Zhou, G.L.Holden, C.Affleck, V.Lamb, R.Newling, K.Ashton, P.Valentine, R.Redfern, C.Erostyak, J.Makkai, G.Ambler, C.A.Whiting, A.Pohl, E.

(2019) ACS Chem Biol 14: 369-377

  • DOI: 10.1021/acschembio.8b00916
  • Primary Citation of Related Structures:  
    5OGB

  • PubMed Abstract: 
  • Retinoids, such as all- trans-retinoic acid (ATRA), are endogenous signaling molecules derived from vitamin A that influence a variety of cellular processes through mediation of transcription events in the cell nucleus. Because of these wide-ranging ...

    Retinoids, such as all- trans-retinoic acid (ATRA), are endogenous signaling molecules derived from vitamin A that influence a variety of cellular processes through mediation of transcription events in the cell nucleus. Because of these wide-ranging and powerful biological activities, retinoids have emerged as therapeutic candidates of enormous potential. However, their use has been limited, to date, due to a lack of understanding of the complex and intricate signaling pathways that they control. We have designed and synthesized a family of synthetic retinoids that exhibit strong, intrinsic, solvatochromatic fluorescence as multifunctional tools to interrogate these important biological activities. We utilized the unique photophysical characteristics of these fluorescent retinoids to develop a novel in vitro fluorometric binding assay to characterize and quantify their binding to their cellular targets, including cellular retinoid binding protein II (CRABPII). The dihydroquinoline retinoid, DC360, exhibited particularly strong binding ( K d = 34.0 ± 2.5 nM), and we further used X-ray crystallography to determine the structure of the DC360-CRABPII complex to 1.8 Å, which showed that DC360 occupies the known hydrophobic retinoid binding pocket. Finally, we used confocal fluorescence microscopy to image the cellular behavior of the compounds in cultured human epithelial cells, highlighting a fascinating nuclear localization, and used RNA sequencing to confirm that the compounds regulate cellular processes similar to those of ATRA. We anticipate that the unique properties of these fluorescent retinoids can now be used to cast new light on the vital and highly complex retinoid signaling pathway.


    Organizational Affiliation

    Department of Biosciences , Durham University , South Road , Durham DH1 3LE , U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cellular retinoic acid-binding protein 2A138Homo sapiensMutation(s): 0 
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
Expand
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9U5
Query on 9U5

Download CCD File 
A
4-[2-(4,4-dimethyl-1-propan-2-yl-quinolin-6-yl)ethynyl]benzoic acid
C23 H23 N O2
HXWVRWZLWIKKOS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.05α = 90
b = 45.58β = 102.87
c = 36.67γ = 90
Software Package:
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
BUCCANEERmodel building
Cootmodel building
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United Kingdom--

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection