6MQY | pdb_00006mqy

Crystal Structure of the 13-cis Product of All-trans Retinal-Bound R111K:Y134F:T54V:R132Q:P39Y:R59Y:L121E Mutant of Human Cellular Retinoic Acid Binding Protein II Irradiated with 400 nm Laser (30 seconds) at 1.9 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.217 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Mimicking Microbial Rhodopsin Isomerization in a Single Crystal.

Ghanbarpour, A.Nairat, M.Nosrati, M.Santos, E.M.Vasileiou, C.Dantus, M.Borhan, B.Geiger, J.H.

(2019) J Am Chem Soc 141: 1735-1741

  • DOI: https://doi.org/10.1021/jacs.8b12493
  • Primary Citation Related Structures: 
    6MOP, 6MOQ, 6MOR, 6MOV, 6MOX, 6MPK, 6MQI, 6MQJ, 6MQW, 6MQX, 6MQY, 6MQZ, 6MR0

  • PubMed Abstract: 

    Bacteriorhodopsin represents the simplest, and possibly most abundant, phototropic system requiring only a retinal-bound transmembrane protein to convert photons of light to an energy-generating proton gradient. The creation and interrogation of a microbial rhodopsin mimic, based on an orthogonal protein system, would illuminate the design elements required to generate new photoactive proteins with novel function. We describe a microbial rhodopsin mimic, created using a small soluble protein as a template, that specifically photoisomerizes all- trans to 13- cis retinal followed by thermal relaxation to the all- trans isomer, mimicking the bacteriorhodopsin photocycle, in a single crystal. The key element for selective isomerization is a tuned steric interaction between the chromophore and protein, similar to that seen in the microbial rhodopsins. It is further demonstrated that a single mutation converts the system to a protein photoswitch without chromophore photoisomerization or conformational change.


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

Macromolecule Content 

  • Total Structure Weight: 16.16 kDa 
  • Atom Count: 1,188 
  • Modeled Residue Count: 137 
  • Deposited Residue Count: 137 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cellular retinoic acid-binding protein 2137Homo sapiensMutation(s): 7 
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.217 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.343α = 90
b = 58.343β = 90
c = 99.865γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-09
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-11
    Changes: Advisory, Data collection, Database references, Refinement description
  • Version 1.4: 2024-10-23
    Changes: Structure summary