4WF0

Crystal Structure of iLID - an Improved Light-Inducible Dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Engineering an improved light-induced dimer (iLID) for controlling the localization and activity of signaling proteins.

Guntas, G.Hallett, R.A.Zimmerman, S.P.Williams, T.Yumerefendi, H.Bear, J.E.Kuhlman, B.

(2015) Proc Natl Acad Sci U S A 112: 112-117

  • DOI: 10.1073/pnas.1417910112
  • Primary Citation of Related Structures:  
    4WF0

  • PubMed Abstract: 
  • The discovery of light-inducible protein-protein interactions has allowed for the spatial and temporal control of a variety of biological processes. To be effective, a photodimerizer should have several characteristics: it should show a large change ...

    The discovery of light-inducible protein-protein interactions has allowed for the spatial and temporal control of a variety of biological processes. To be effective, a photodimerizer should have several characteristics: it should show a large change in binding affinity upon light stimulation, it should not cross-react with other molecules in the cell, and it should be easily used in a variety of organisms to recruit proteins of interest to each other. To create a switch that meets these criteria we have embedded the bacterial SsrA peptide in the C-terminal helix of a naturally occurring photoswitch, the light-oxygen-voltage 2 (LOV2) domain from Avena sativa. In the dark the SsrA peptide is sterically blocked from binding its natural binding partner, SspB. When activated with blue light, the C-terminal helix of the LOV2 domain undocks from the protein, allowing the SsrA peptide to bind SspB. Without optimization, the switch exhibited a twofold change in binding affinity for SspB with light stimulation. Here, we describe the use of computational protein design, phage display, and high-throughput binding assays to create an improved light inducible dimer (iLID) that changes its affinity for SspB by over 50-fold with light stimulation. A crystal structure of iLID shows a critical interaction between the surface of the LOV2 domain and a phenylalanine engineered to more tightly pin the SsrA peptide against the LOV2 domain in the dark. We demonstrate the functional utility of the switch through light-mediated subcellular localization in mammalian cell culture and reversible control of small GTPase signaling.


    Related Citations: 
    • Designing photoswitchable peptides using the AsLOV2 domain.
      Lungu, O.I., Hallett, R.A., Choi, E.J., Aiken, M.J., Hahn, K.M., Kuhlman, B.
      (2012) Chem Biol --: 507

    Organizational Affiliation

    Department of Biochemistry & Biophysics, University of North Carolina Lineberger Comprehensive Cancer Center, and bkuhlman@email.unc.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NPH1-1A, B158Avena sativaMutation(s): 11 
Gene Names: NPH1-1
Find proteins for O49003 (Avena sativa)
Explore O49003 
Go to UniProtKB:  O49003
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.156α = 90
b = 70.339β = 90
c = 80.378γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM093208

Revision History 

  • Version 1.0: 2014-12-24
    Type: Initial release
  • Version 1.1: 2015-01-07
    Changes: Database references
  • Version 1.2: 2015-01-14
    Changes: Database references
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy