8VZY

Q108K:K40L:T51V:T53S:R58Y mutant of hCRBPII bound to synthetic fluorophore TD-1V


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Regulation of Absorption and Emission in a Protein/Fluorophore Complex.

Santos, E.M.Chandra, I.Assar, Z.Sheng, W.Ghanbarpour, A.Bingham, C.Vasileiou, C.Geiger, J.H.Borhan, B.

(2024) ACS Chem Biol 19: 1725-1732

  • DOI: https://doi.org/10.1021/acschembio.4c00125
  • Primary Citation of Related Structures:  
    8VZX, 8VZY, 8VZZ, 8W00, 8W02

  • PubMed Abstract: 

    Human cellular retinol binding protein II (hCRBPII) was used as a protein engineering platform to rationally regulate absorptive and emissive properties of a covalently bound fluorogenic dye. We demonstrate the binding of a thio-dapoxyl analog via formation of a protonated imine between an active site lysine residue and the chromophore's aldehyde. Rational manipulation of the electrostatics of the binding pocket results in a 204 nm shift in absorption and a 131 nm shift in emission. The protein is readily expressed in mammalian systems and binds with exogenously delivered fluorophore as demonstrated by live-cell imaging experiments.


  • 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
Retinol-binding protein 2
A, B
133Homo sapiensMutation(s): 5 
Gene Names: RBP2CRBP2
UniProt & NIH Common Fund Data Resources
Find proteins for P50120 (Homo sapiens)
Explore P50120 
Go to UniProtKB:  P50120
PHAROS:  P50120
GTEx:  ENSG00000114113 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50120
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.34 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.238 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.289α = 92.51
b = 35.252β = 90.49
c = 64.872γ = 111.72
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Database references
  • Version 1.2: 2024-08-28
    Changes: Database references
  • Version 1.3: 2024-09-04
    Changes: Database references
  • Version 1.4: 2024-11-13
    Changes: Structure summary