4M6S | pdb_00004m6s

Crystal structure of the R111K:R132Y:Y134F:T54V:R59W:A32W mutant of the Cellular Retinoic Acid Binding Protein Type II in complex with All-Trans Retinal at 2.38 Angstrom Resolution

• PDB DOI: https://doi.org/10.2210/pdb4M6S/pdb

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


• Deposited: 2013-08-10 Released: 2013-10-09 
• Deposition Author(s): Nosrati, M., Geiger, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free: 
  0.235 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Starting Model: experimental

Literature

Rational Design of a Colorimetric pH Sensor from a Soluble Retinoic Acid Chaperone.

Berbasova, T., Nosrati, M., Vasileiou, C., Wang, W., Lee, K.S., Yapici, I., Geiger, J.H., Borhan, B.

(2013) J Am Chem Soc 135: 16111-16119

• PubMed: 24059243 
• DOI: https://doi.org/10.1021/ja404900k
• Primary Citation Related Structures: 
  4I9R, 4I9S, 4M6S, 4M7M


• PubMed Abstract: 
  

  Reengineering of cellular retinoic acid binding protein II (CRABPII) to be capable of binding retinal as a protonated Schiff base is described. Through rational alterations of the binding pocket, electrostatic perturbations of the embedded retinylidene chromophore that favor delocalization of the iminium charge lead to exquisite control in the regulation of chromophoric absorption properties, spanning the visible spectrum (474-640 nm). The pKa of the retinylidene protonated Schiff base was modulated from 2.4 to 8.1, giving rise to a set of proteins of varying colors and pH sensitivities. These proteins were used to demonstrate a concentration-independent, ratiometric pH sensor.

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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.

Macromolecule Content 

• Total Structure Weight: 15.97 kDa 
• Atom Count: 1,150 
• Modeled Residue Count: 137 
• Deposited Residue Count: 137 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellular retinoic acid-binding protein 2	A	137	Homo sapiens	Mutation(s): 6  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
RET	B [auth A]	RETINAL C20 H28 O NCYCYZXNIZJOKI-OVSJKPMPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.47 Å
• R-Value Free:  0.235 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.629	α = 90
b = 56.629	β = 90
c = 111.318	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-09 
Deposition Author(s): Nosrati, M., Geiger, J.H.

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 1.1: 2014-02-19
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-30
  Changes: Structure summary