4YBU

Crystal structure of the R111K:Y134F:T54V:R132Q:P39Q:R59Y mutant of human Cellular Retinoic Acid Binding ProteinII in complex with Retinal after 24 h incubation and 1 hour UV irradiation at 1.92 angstrom - 1st cycle


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

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:  
    4YBU, 4YBP, 4YCH, 4YCE, 4YDA, 4YDB, 4YFQ, 4YFR, 4YFP, 4YGZ

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cellular retinoic acid-binding protein 2A137Homo sapiensMutation(s): 6 
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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.326α = 90
b = 58.326β = 90
c = 99.936γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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