6E5R

Crystal structure of the apo domain-swapped dimer Q108K:T51D:A28C mutant of human Cellular Retinol Binding Protein II

• PDB DOI:  https://doi.org/10.2210/pdb6E5R/pdb

• Classification: LIPID BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Bacterial expression vector pBEN1-SGC
• Mutation(s): Yes 


• Deposited: 2018-07-22 Released: 2019-08-07 
• Deposition Author(s): Ghanbarpour, A., Geiger, J.
• Funding Organization(s): National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.281 
• R-Value Work: 0.229 
• R-Value Observed: 0.235 

Literature

Engineering the hCRBPII Domain-Swapped Dimer into a New Class of Protein Switches.

Ghanbarpour, A., Pinger, C., Esmatpour Salmani, R., Assar, Z., Santos, E.M., Nosrati, M., Pawlowski, K., Spence, D., Vasileiou, C., Jin, X., Borhan, B., Geiger, J.H.

(2019) J Am Chem Soc 141: 17125-17132

• PubMed: 31557439 
• DOI: https://doi.org/10.1021/jacs.9b04664
• Primary Citation of Related Structures:  
  6E50, 6E51, 6E5E, 6E5Q, 6E5R, 6E5S, 6E6L, 6E7M, 6MCU, 6MCV, 6MKV, 6MLB, 6ON5, 6ON7, 6ON8


• PubMed Abstract: 
  

Protein conformational switches or allosteric proteins play a key role in the regulation of many essential biological pathways. Nonetheless, the implementation of protein conformational switches in protein design applications has proven challenging, with only a few known examples that are not derivatives of naturally occurring allosteric systems. We have discovered that the domain-swapped (DS) dimer of hCRBPII undergoes a large and robust conformational change upon retinal binding, making it a potentially powerful template for the design of protein conformational switches. Atomic resolution structures of the apo- and holo-forms illuminate a simple, mechanical movement involving sterically driven torsion angle flipping of two residues that drive the motion. We further demonstrate that the conformational "readout" can be altered by addition of cross-domain disulfide bonds, also visualized at atomic resolution. Finally, as a proof of principle, we have created an allosteric metal binding site in the DS dimer, where ligand binding results in a reversible 5-fold loss of metal binding affinity. The high resolution structure of the metal-bound variant illustrates a well-formed metal binding site at the interface of the two domains of the DS dimer and confirms the design strategy for allosteric regulation.

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Organizational Affiliation: 

Department of Chemistry , Michigan State University , East Lansing , Michigan 48824 , United States.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 31.93 kDa 
• Atom Count: 2,285 
• Modelled 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): 3  Gene Names: RBP2, CRBP2
UniProt & NIH Common Fund Data Resources
Find proteins for P50120 (Homo sapiens) Explore P50120  Go to UniProtKB:  P50120
PHAROS:  P50120

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A], E [auth A], F [auth A], I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	C [auth A], G [auth B], H [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.59 Å
• R-Value Free: 0.281 
• R-Value Work: 0.229 
• R-Value Observed: 0.235 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 30.857	α = 90
b = 68.182	β = 90
c = 130.04	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-08-07 
Deposition Author(s): Ghanbarpour, A., Geiger, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)	United States	--

Revision History  

• Version 1.0: 2019-08-07
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection, Database references
• Version 1.2: 2019-11-13
  Changes: Data collection, Database references
• Version 1.3: 2019-12-18
  Changes: Author supporting evidence