› 6lqf

X-ray diffraction
1.5Å resolution

Crystal structure of Arabidopsis ARID5 ARID-PHD cassette in complex with H3K4me3 peptide and DNA

Released:
DOI: 10.2210/pdb6lqf/pdb
PDB entry 6lqf coloured by chain, front view.
PDB entry 6lqf coloured by chain, side view.
PDB entry 6lqf coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Dual Recognition of H3K4me3 and DNA by the ISWI Component ARID5 Regulates the Floral Transition in Arabidopsis.
Tan LM, Liu R, Gu BW, Zhang CJ, Luo J, Guo J, Wang Y, Chen L, Du X, Li S, Shao CR, Su YN, Cai XW, Lin RN, Li L, Chen S, Du J, He XJ
Plant Cell 32 2178-2195 (2020)
PMID: 32358072

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120224 (preferred)
Entry contents:
2 distinct polypeptide molecules
1 distinct DNA molecule
Macromolecules (3 distinct):
AT-rich interactive domain-containing protein 4 Chain: A
Molecule details ›
Chain: A
Length: 204 amino acids
Theoretical weight: 22.94 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6NQ79 (Residues: 545-747; Coverage: 27%)
Gene names: ARID4, At3g43240, F7K15.90
Sequence domains: ARID/BRIGHT DNA binding domain
Histone H3.1 Chain: P
Molecule details ›
Chain: P
Length: 15 amino acids
Theoretical weight: 1.61 KDa
Source organism: Arabidopsis thaliana
Expression system: Not provided
UniProt:
  • Canonical: P59226 (Residues: 2-16; Coverage: 11%)
Gene names: At1g09200, At3g27360, At5g10390, At5g10400, At5g65360, F12B17_250, F12B17_260, HTR1, HTR13, HTR2, HTR3, HTR9, K1G2.8, MNA5.9, T12M4.9
DNA (5'-D(*TP*TP*TP*AP*GP*AP*TP*CP*TP*AP*AP*A)-3') Chains: B, C
Molecule details ›
Chains: B, C
Length: 12 nucleotides
Theoretical weight: 3.66 KDa

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
1 modified residue:
Ligand M3L 1 x M3L

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 56.173Å b: 59.428Å c: 92.958Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.175 0.192
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Biological role and mechanism of chromatin readers in plants.
Scheid et al. (2021)
2 more

1 mention without citation

Continuous Automated Model EvaluatiOn (CAMEO)-Perspectives on the future of fully automated evaluation of structure prediction methods.
Robin et al. (2021)