4YDB

Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Retinoic Acid Binding Protein II in complex with Retinal at 2.03 angstrom -UV irradiated crystal- 3rd cycle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Photoisomerizing Rhodopsin Mimic Observed at Atomic Resolution.

Nosrati, M.Berbasova, T.Vasileiou, C.Borhan, B.Geiger, J.H.

(2016) J.Am.Chem.Soc. 138: 8802-8808

  • DOI: 10.1021/jacs.6b03681
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The members of the rhodopsin family of proteins are involved in many essential light-dependent processes in biology. Specific photoisomerization of the protein-bound retinylidene PSB at a specified wavelength range of light is at the heart of all of ...

    The members of the rhodopsin family of proteins are involved in many essential light-dependent processes in biology. Specific photoisomerization of the protein-bound retinylidene PSB at a specified wavelength range of light is at the heart of all of these systems. Nonetheless, it has been difficult to reproduce in an engineered system. We have developed rhodopsin mimics, using intracellular lipid binding protein family members as scaffolds, to study fundamental aspects of protein/chromophore interactions. Herein we describe a system that specifically isomerizes the retinylidene protonated Schiff base both thermally and photochemically. This isomerization has been characterized at atomic resolution by quantitatively interconverting the isomers in the crystal both thermally and photochemically. This event is accompanied by a large pKa change of the imine similar to the pKa changes observed in bacteriorhodopsin and visual opsins during isomerization.


    Organizational Affiliation

    Department of Chemistry, Michigan State University , East Lansing, Michigan 48824, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cellular retinoic acid-binding protein 2
A
137Homo sapiensMutation(s): 6 
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
RET
Query on RET

Download SDF File 
Download CCD File 
A
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.206 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 58.655α = 90.00
b = 58.655β = 90.00
c = 100.352γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-03-09
    Type: Structure summary
  • Version 1.2: 2016-06-29
    Type: Database references
  • Version 1.3: 2016-08-03
    Type: Database references