8W02 | pdb_00008w02

Q108K:K40L:T51V:T53S:R58W mutant of hCRBPII bound to synthetic fluorophore TD-1V

• PDB DOI: https://doi.org/10.2210/pdb8W02/pdb

• Classification: RETINOL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-02-13 Released: 2024-04-03 
• Deposition Author(s): Ghanbarpour, A., Geiger, J.H., Borhan, B.
• Funding Organization(s): National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.209 (DCC) 

Starting Model: experimental

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

• PubMed: 39046136 
• DOI: https://doi.org/10.1021/acschembio.4c00125
• Primary Citation 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 31.58 kDa 
• Atom Count: 2,282 
• Modeled Residue Count: 266 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinol-binding protein 2	A, B	133	Homo sapiens	Mutation(s): 5  Gene Names: RBP2, CRBP2
UniProt & NIH Common Fund Data Resources
Find proteins for P50120 (Homo sapiens) Explore P50120  Go to UniProtKB:  P50120
PHAROS:  P50120 GTEx:  ENSG00000114113

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AEQ	D [auth B]	(2E)-3-{5-[4-(dimethylamino)phenyl]thiophen-2-yl}but-2-enal C16 H17 N O S LFXNQATVKSUQRE-ZRDIBKRKSA-N
ACT	C [auth A], E [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.237 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.209 (DCC) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.889	α = 90.32
b = 36.209	β = 91.86
c = 64.081	γ = 113.62

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-04-03 
Deposition Author(s): Ghanbarpour, A., Geiger, J.H., Borhan, B.

---

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

Revision History  

• 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: 2024-10-09
  Changes: Structure summary