5DJU | pdb_00005dju

Crystal structure of LOV2 (C450A) domain in complex with Zdk3

• PDB DOI: https://doi.org/10.2210/pdb5DJU/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Staphylococcus aureus, Avena sativa
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-09-02 Released: 2016-07-20 
• Deposition Author(s): Tarnawski, M., Wang, H., Yumerefendi, H., Hahn, K.M., Schlichting, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Models: experimental

Literature

LOVTRAP: an optogenetic system for photoinduced protein dissociation.

Wang, H., Vilela, M., Winkler, A., Tarnawski, M., Schlichting, I., Yumerefendi, H., Kuhlman, B., Liu, R., Danuser, G., Hahn, K.M.

(2016) Nat Methods 13: 755-758

• PubMed: 27427858 
• DOI: https://doi.org/10.1038/nmeth.3926
• Primary Citation Related Structures: 
  5DJT, 5DJU, 5EFW


• PubMed Abstract: 
  

  LOVTRAP is an optogenetic approach for reversible light-induced protein dissociation using protein A fragments that bind to the LOV domain only in the dark, with tunable kinetics and a >150-fold change in the dissociation constant (Kd). By reversibly sequestering proteins at mitochondria, we precisely modulated the proteins' access to the cell edge, demonstrating a naturally occurring 3-mHz cell-edge oscillation driven by interactions of Vav2, Rac1, and PI3K proteins.

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Organizational Affiliation: 
• Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, Texas, USA.
Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany.
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
Lineberger Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48 kDa 
• Atom Count: 3,519 
• Modeled Residue Count: 400 
• Deposited Residue Count: 412 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Engineered protein, Zdk3 affibody	A [auth B], C [auth D]	61	Staphylococcus aureus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NPH1-2	B [auth A], D [auth C]	145	Avena sativa	Mutation(s): 1  Gene Names: NPH1-2 EC: 2.7.11.1
UniProt
Find proteins for O49004 (Avena sativa) Explore O49004  Go to UniProtKB:  O49004

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A], I [auth C]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
CL	F [auth A], G [auth A], H [auth A], J [auth C], K [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.207 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.24	α = 90
b = 74.5	β = 90
c = 81.91	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Tarnawski, M., Wang, H., Yumerefendi, H., Hahn, K.M., Schlichting, I.

Revision History  

• Version 1.0: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2016-07-27
  Changes: Database references
• Version 1.2: 2016-09-07
  Changes: Database references
• Version 1.3: 2024-01-10
  Changes: Data collection, Database references, Refinement description