› 5z8n

X-ray diffraction
3.1Å resolution

Crystal structure of Arabidopsis thaliana EBS C-terminal deletion construct in complex with an H3K4me2 peptide

Released:
DOI: 10.2210/pdb5z8n/pdb
PDB entry 5z8n coloured by chain, front view.
PDB entry 5z8n coloured by chain, side view.
PDB entry 5z8n coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
EBS is a bivalent histone reader that regulates floral phase transition in Arabidopsis.
Yang Z, Qian S, Scheid RN, Lu L, Chen X, Liu R, Du X, Lv X, Boersma MD, Scalf M, Smith LM, Denu JM, Du J, Zhong X
Nat Genet 50 1247-1253 (2018)
PMID: 30082787

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-123481 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Chromatin remodeling protein EBS Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 199 amino acids
Theoretical weight: 22.65 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: F4JL28 (Residues: 1-199; Coverage: 85%)
Gene names: At4g22140, EBS, F1N20.240
Sequence domains:
Histone H3.1 Chains: P, Q, R
Molecule details ›
Chains: P, Q, R
Length: 15 amino acids
Theoretical weight: 1.59 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

Ligands and Environments

1 bound ligand:
Ligand ZN 6 x ZN
1 modified residue:
Ligand MLY 3 x MLY

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P21
Unit cell:
a: 73.464Å b: 75.696Å c: 80.357Å
α: 90° β: 115.41° γ: 90°
R-values:
R R work R free
0.215 0.213 0.252
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

19 review citations

Polycomb Gene Silencing Mechanisms: PRC2 Chromatin Targeting, H3K27me3 'Readout', and Phase Separation-Based Compaction.
Guo et al. (2021)
18 more

2 mentions without citation

Creativity comes from interactions: modules of protein interactions in plants.
Allen et al. (2022)
1 more