6ON5

Crystal Structure of the Zn-bound Domain-Swapped Dimer Q108K:T51D:A28C:L36C:F57H Mutant of Human Cellular Retinol Binding Protein II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.638 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1021/jacs.9b04664
  • Primary Citation of Related Structures:  

  • 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, ...

    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 mechanism involving sterically driven torsion angle flipping of two residues that drive the motion. We further demonstrate that the con-formational "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 five-fold loss of metal binding affinity. The high resolution structure of the metal-bound variant illustrates a well-formed metal binding site at the inter-face of the two domains of the DS dimer, and confirms the design strategy for allosteric regulation.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinol-binding protein 2
A, B
133Homo sapiensMutation(s): 5 
Gene Names: RBP2 (CRBP2)
Find proteins for P50120 (Homo sapiens)
Go to Gene View: RBP2
Go to UniProtKB:  P50120
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.638 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.416α = 90.00
b = 61.759β = 90.00
c = 72.638γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

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