5EFW

Crystal structure of LOV2-Zdk1 - the complex of oat LOV2 and the affibody protein Zdark1

• PDB DOI: https://doi.org/10.2210/pdb5EFW/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Avena sativa, Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-10-26 Released: 2016-07-20 
• Deposition Author(s): Winkler, A., Wang, H., Hartmann, E., Hahn, K., Schlichting, I.
• Funding Organization(s): German Research Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

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 of 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 30.8 kDa 
• Atom Count: 2,114 
• Modelled Residue Count: 245 
• Deposited Residue Count: 265 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NPH1-1	A	145	Avena sativa	Mutation(s): 1  Gene Names: NPH1-1 EC: 2.7.11.1
UniProt
Find proteins for O49003 (Avena sativa) Explore O49003  Go to UniProtKB:  O49003

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Z-dark, a small protein based on the Z domain affibody	B, C	60	Staphylococcus aureus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	D [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
SO4	E [auth A], F [auth A], G [auth A], H [auth A], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.257 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.7	α = 90
b = 54.7	β = 90
c = 188.03	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Coot	model building
PHENIX	refinement
PDB_EXTRACT	data extraction
XSCALE	data scaling
PHASER	phasing
XSCALE	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-20 
Deposition Author(s): Winkler, A., Wang, H., Hartmann, E., Hahn, K., Schlichting, I.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	FOR1279

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: 2018-01-31
  Changes: Author supporting evidence, Database references
• Version 1.4: 2024-01-10
  Changes: Data collection, Database references, Refinement description