4HHD

2.75 Angstrom resolution crystal structure of the A. thaliana LOV2 domain with an extended N-terminal A' helix (cryo dark structure)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Coiled-coil dimerization of the LOV2 domain of the blue-light photoreceptor phototropin 1 from Arabidopsis thaliana.

Halavaty, A.S.Moffat, K.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 1316-1321

  • DOI: https://doi.org/10.1107/S1744309113029199
  • Primary Citation of Related Structures:  
    4HHD

  • PubMed Abstract: 

    A key role in signal transduction and dimerization mediated by Per-Arnt-Sim (PAS) domains is played by α-helical linkers that flank the structurally similar α/β cores of these domains. However, crystal-packing forces and the different construct lengths and sequences of the PAS domains influence the final length and orientation of the linkers relative to the core and create uncertainty in the exact mechanism of the linker function. Thus, structural characterization and comparison of the linkers within isolated PAS-domain constructs and/or full-length PAS-containing proteins is important for clarification of the mechanism. The plant blue-light photoreceptors phototropins possess two N-terminal flavin mononucleotide-based light, oxygen or voltage (LOV) domains (LOV1 and LOV2) that comprise a subclass of the PAS family and one C-terminal serine/threonine kinase domain whose enzymatic activity is regulated by blue light. The dark-adapted state crystal structures of the Arabidopsis thaliana phototropin 1 and phototropin 2 LOV1-domain constructs flanked by an N-terminal A'α helix and the structure of the phototropin 2 core LOV2 domain are known. Here, the crystal structure of the A. thaliana phototropin 1 LOV2 domain has been determined in its dark-adapted state. The core is flanked by an N-terminal A'α helix and a C-terminal Jα helix similar to those in the previously reported structure of Avena sativa phototropin 1 LOV2. In contrast to the monomeric A. sativa LOV2, A. thaliana LOV2 is a dimer in which two A'α helices adopt a scissor-like orientation at the dimer interface and form a short α-helical coiled coil. The Jα helix predominantly interacts with the β-sheet and plays a role in coiled-coil formation and dimerization.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL 60637, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phototropin-1
A, B
166Arabidopsis thalianaMutation(s): 0 
Gene Names: PHOT1JK224NPH1RPT1At3g45780T6D9_110
EC: 2.7.11.1
UniProt
Find proteins for O48963 (Arabidopsis thaliana)
Explore O48963 
Go to UniProtKB:  O48963
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO48963
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.234 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.382α = 90
b = 63.382β = 90
c = 171.318γ = 90
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-09
    Type: Initial release
  • Version 1.1: 2013-12-11
    Changes: Database references
  • Version 1.2: 2014-02-12
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description