5A8B | pdb_00005a8b

Structure of a parallel dimer of the aureochrome 1a LOV domain from Phaeodactylum tricornutum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free: 
    0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Structure of a Native-Like Aureochrome 1A Lov Domain Dimer from Phaeodactylum Tricornutum.

Banerjee, A.Herman, E.Kottke, T.Essen, L.O.

(2016) Structure 24: 171

  • DOI: https://doi.org/10.1016/j.str.2015.10.022
  • Primary Citation Related Structures: 
    5A8B

  • PubMed Abstract: 

    Light-oxygen-voltage (LOV) domains absorb blue light for mediating various biological responses in all three domains of life. Aureochromes from stramenopile algae represent a subfamily of photoreceptors that differs by its inversed topology with a C-terminal LOV sensor and an N-terminal effector (basic region leucine zipper, bZIP) domain. We crystallized the LOV domain including its flanking helices, A'α and Jα, of aureochrome 1a from Phaeodactylum tricornutum in the dark state and solved the structure at 2.8 Å resolution. Both flanking helices contribute to the interface of the native-like dimer. Small-angle X-ray scattering shows light-induced conformational changes limited to the dimeric envelope as well as increased flexibility in the lit state for the flanking helices. These rearrangements are considered to be crucial for the formation of the light-activated dimer. Finally, the LOV domain of the class 2 aureochrome PtAUREO2 was shown to lack a chromophore because of steric hindrance caused by M301.


  • Organizational Affiliation
    • Structural Biochemistry - Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany.

Macromolecule Content 

  • Total Structure Weight: 73.96 kDa 
  • Atom Count: 4,322 
  • Modeled Residue Count: 533 
  • Deposited Residue Count: 648 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PTAUREO1A LOV2 DOMAIN
A, B, C, D
162Phaeodactylum tricornutumMutation(s): 0 
UniProt
Find proteins for A0A140UHJ0 (Phaeodactylum tricornutum)
Explore A0A140UHJ0 
Go to UniProtKB:  A0A140UHJ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A140UHJ0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN

Query on FMN



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
H [auth C],
J [auth D]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
K [auth D]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
F [auth B],
I [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.79 Å
  • R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.391α = 90
b = 75.55β = 94.73
c = 77.664γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description