› 5zwx

X-ray diffraction
1.9Å resolution

Crystal structure of Raphanus sativus AGDP1 AGD12 in complex with an H3K9me2 peptide

Released:
DOI: 10.2210/pdb5zwx/pdb
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PDB entry 5zwx coloured by chain, front view.
PDB entry 5zwx coloured by chain, side view.
PDB entry 5zwx coloured by chain, top view.
Source organisms:
Primary publication:
Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin.
Zhang C, Du X, Tang K, Yang Z, Pan L, Zhu P, Luo J, Jiang Y, Zhang H, Wan H, Wang X, Wu F, Tao WA, He XJ, Zhang H, Bressan RA, Du J, Zhu JK
OpenAccess logo Nat Commun 9 4547 (2018)
PMID: 30382101

Function and Biology Details

Biochemical function:
  • not assigned
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-105114 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Agenet domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 161 amino acids
Theoretical weight: 18.63 KDa
Source organism: Raphanus sativus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A0A493R6M0 (Residues: 1-161; Coverage: 100%)
Sequence domains: Agenet domain
Histone H3.1 Chains: P, Q
Molecule details ›
Chains: P, Q
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

No bound ligands
2 modified residues:
Ligand MSE 6 x MSE
Ligand MLY 2 x MLY

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL18U1
Spacegroup: P21
Unit cell:
a: 47.653Å b: 54.981Å c: 83.576Å
α: 90° β: 99.72° γ: 90°
R-values:
R R work R free
0.183 0.182 0.211
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

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Citations

13 review citations

Interactions between metabolism and chromatin in plant models.
Lindermayr et al. (2020)
12 more

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