7RY5 | pdb_00007ry5

Cellular Retinoic Acid Binding Protein II with Bound Inhibitor 4-[6-({4-[(fluorosulfonyl)oxy]phenyl}ethynyl)-4,4-dimethyl-3,4-dihydroquinolin-1(2H)-yl]-4-oxobutanoic acid

• PDB DOI: https://doi.org/10.2210/pdb7RY5/pdb

• Classification: SIGNALING PROTEIN/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2021-08-24 Released: 2021-12-15 
• Deposition Author(s): Kimmel, B.R., Mrksich, M.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.243 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.185 (DCC) 

Starting Model: experimental

Literature

Development of an Enzyme-Inhibitor Reaction Using Cellular Retinoic Acid Binding Protein II for One-Pot Megamolecule Assembly.

Kimmel, B.R., Mrksich, M.

(2021) Chemistry 27: 17843-17848

• PubMed: 34713526 
• DOI: https://doi.org/10.1002/chem.202103059
• Primary Citation Related Structures: 
  7RY5


• PubMed Abstract: 
  

  This paper presents an enzyme building block for the assembly of megamolecules. The system is based on the inhibition of the human-derived cellular retinoic acid binding protein II (CRABP2) domain. We synthesized a synthetic retinoid bearing an arylfluorosulfate group, which uses sulfur fluoride exchange click chemistry to covalently inhibit CRABP2. We conjugated both the inhibitor and a fluorescein tag to an oligo(ethylene glycol) backbone and measured a second-order rate constant for the protein inhibition reaction of approximately 3,600 M ^-1 s ^-1 . We used this new enzyme-inhibitor pair to assemble multi-protein structures in one-pot reactions using three orthogonal assembly chemistries to demonstrate exact control over the placement of protein domains within a single, homogeneous molecule. This work enables a new dimension of control over specificity, orientation, and stoichiometry of protein domains within atomically precise nanostructures.

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Organizational Affiliation: 
• Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.
Department of Biomedical Engineering, Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA.

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.

Macromolecule Content 

• Total Structure Weight: 35.71 kDa 
• Atom Count: 2,550 
• Modeled Residue Count: 281 
• Deposited Residue Count: 302 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular retinoic acid-binding protein 2	A [auth AAA], B [auth BBB]	151	Homo sapiens	Mutation(s): 0  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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
80V (Subject of Investigation/LOI)	C [auth AAA], D [auth BBB]	4-[6-({4-[(fluorosulfonyl)oxy]phenyl}ethynyl)-4,4-dimethyl-3,4-dihydroquinolin-1(2H)-yl]-4-oxobutanoic acid C23 H22 F N O6 S OJLXEIKKMUTWLF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.233 (Depositor), 0.243 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.185 (DCC) 

Diffraction Data: https://doi.org/10.2210/image_data.cif

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.604	α = 90
b = 69.655	β = 90
c = 120.845	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-12-15 
Deposition Author(s): Kimmel, B.R., Mrksich, M.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	DGE-1842165

Revision History  

• Version 1.0: 2021-12-15
  Type: Initial release
  
• Version 1.1: 2022-01-05
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2024-11-06
  Changes: Structure summary