The structure and function of the DNA binding domain of class B MpARF2 share more traits with class A AtARF5 than to that of class B AtARF1

Isidro Crespo.

SASDVU5 – Marchantia polymorpha Auxin Response Factor 3 in complex with high affinity DNA

Auxin response factor
High Affinity ARF binding sequence inverted repeat with 6 nucleotide spacing
MWexperimental 42850 kDa
MWexpected 58 kDa
VPorod 67 nm3
log I(s) 2.68×100 2.68×10-1 2.68×10-2 2.68×10-3
Auxin response factor High Affinity ARF binding sequence inverted repeat with 6 nucleotide spacing small angle scattering data  s, nm-1
ln I(s)
Auxin response factor High Affinity ARF binding sequence inverted repeat with 6 nucleotide spacing Guinier plot ln 2.68×100 Rg: 3.1 nm 0 (3.1 nm)-2 s2
(sRg)2I(s)/I(0)
Auxin response factor High Affinity ARF binding sequence inverted repeat with 6 nucleotide spacing Kratky plot 1.104 0 √3 sRg
p(r)
Auxin response factor High Affinity ARF binding sequence inverted repeat with 6 nucleotide spacing pair distance distribution function Rg: 3 nm 0 Dmax: 8.4 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Auxin response factor High Affinity ARF binding sequence inverted repeat with 6 nucleotide spacing SWISSMODEL model
Synchrotron SAXS data from solutions of M. polymorpha auxin response factor 3 in complex with high affinity DNA in 20 mM Tris-HCl, 150 mM NaCl, 1 mM DTT, pH 8 were collected on the BL11 - NCD beam line at ALBA (Cerdanyola del Vallès, Barcelona, Spain) using a ADSC Quantum 210r detector at a sample-detector distance of 2.6 m and at a wavelength of λ = 0.1 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 3.50 mg/ml was measured at 20°C. 20 successive 0.500 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

CAUTION: Dmax appears underestimated.

Auxin response factor (MpARF3)
Mol. type   Protein
Organism   Marchantia polymorpha
Olig. state   Monomer
Mon. MW   45.5 kDa
 
UniProt   A0A0G3FJH3 (52-470)
Sequence   FASTA
 
High Affinity ARF binding sequence inverted repeat with 6 nucleotide spacing (HA6)
Mol. type   DNA
Olig. state   Dimer
Mon. MW   6.2 kDa
Sequence   FASTA