Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y:A32Y:F3Q mutant of human Cellular Retinoic Acid Binding Protein II with Retinal at 1.58 angstrom resolution

Experimental Data Snapshot

  • Resolution: 1.57 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1021/jacs.6b03681
  • Primary Citation of Related Structures:  
    4YBP, 4YBU, 4YCE, 4YCH, 4YDA, 4YDB, 4YFP, 4YFQ, 4YFR, 4YGG, 4YGH, 4YGZ, 4YH0, 4YKM, 4YKO

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular retinoic acid-binding protein 2
A, B
137Homo sapiensMutation(s): 8 
Gene Names: CRABP2
UniProt & NIH Common Fund Data Resources
Find proteins for P29373 (Homo sapiens)
Explore P29373 
Go to UniProtKB:  P29373
PHAROS:  P29373
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29373
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.57 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.737α = 86.78
b = 39.21β = 79.88
c = 58.402γ = 70.83
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references
  • Version 1.2: 2016-08-03
    Changes: Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description