8VZX

Q108K:K40L:T53A:R58F mutant of hCRBPII bound to synthetic fluorophore TD-1V

• PDB DOI: https://doi.org/10.2210/pdb8VZX/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): Nossoni, Z., Bingham, C.R., Geiger, J.H.
• Funding Organization(s): National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.263 
• R-Value Work: 0.233 

Literature

Regulation of Emission via a Protein-Bound Fluorophore

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

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.95 kDa 
• Atom Count: 4,818 
• Modelled Residue Count: 532 
• Deposited Residue Count: 532 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Retinol-binding protein 2	A, B, C, D	133	Homo sapiens	Mutation(s): 4  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 (Subject of Investigation/LOI)	H [auth C], J [auth D]	(2E)-3-{5-[4-(dimethylamino)phenyl]thiophen-2-yl}but-2-enal C16 H17 N O S LFXNQATVKSUQRE-ZRDIBKRKSA-N
ACT	E [auth A], F [auth B], G [auth C], I [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.47 Å
• R-Value Free: 0.263 
• R-Value Work: 0.233 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.451	α = 109.94
b = 55.167	β = 98.49
c = 69.876	γ = 101.41

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): Nossoni, Z., Bingham, C.R., Geiger, J.H.

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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