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 

Starting Model: experimental
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This is version 1.5 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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cellular retinoic acid-binding protein 2137Homo sapiensMutation(s): 6 
Gene Names: CRABP2
UniProt & NIH Common Fund Data Resources
Find proteins for P29373 (Homo sapiens)
Explore P29373 
Go to UniProtKB:  P29373
PHAROS:  P29373
GTEx:  ENSG00000143320 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29373
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RET
Query on RET

Download Ideal Coordinates CCD File 
B [auth A]RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-10-16
    Changes: Structure summary