› 6fud

X-ray diffraction
1.3Å resolution

Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikA with the HMA domain of Pikm-1 from rice (Oryza sativa)

Released:
DOI: 10.2210/pdb6fud/pdb
PDB entry 6fud coloured by chain, front view.
PDB entry 6fud coloured by chain, side view.
PDB entry 6fud coloured by chain, top view.
Source organisms:
Primary publication:
Polymorphic residues in rice NLRs expand binding and response to effectors of the blast pathogen.
De la Concepcion JC, Franceschetti M, Maqbool A, Saitoh H, Terauchi R, Kamoun S, Banfield MJ
Nat Plants 4 576-585 (2018)
PMID: 29988155

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-110251 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Disease resistance protein Pikm1-TS Chain: A
Molecule details ›
Chain: A
Length: 81 amino acids
Theoretical weight: 8.55 KDa
Source organism: Oryza sativa Japonica Group
Expression system: Escherichia coli
UniProt:
  • Canonical: B5UBC1 (Residues: 186-264; Coverage: 7%)
Gene names: PI-KM1, PIKM1-TS
Structure domains: Alpha-Beta Plaits
AVR-Pikm protein Chain: B
Molecule details ›
Chain: B
Length: 93 amino acids
Theoretical weight: 10.84 KDa
Source organism: Pyricularia oryzae
Expression system: Escherichia coli
UniProt:
  • Canonical: C4B8B9 (Residues: 22-113; Coverage: 100%)
Gene names: AVR-Pik, AVR-Pikm

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P21
Unit cell:
a: 30.07Å b: 54.44Å c: 46.64Å
α: 90° β: 104.43° γ: 90°
R-values:
R R work R free
0.127 0.125 0.162
Expression system: Escherichia coli

Quick links

Citations

16 review citations

Genetic strategies for improving crop yields.
Bailey-Serres et al. (2019)
15 more

3 mentions without citation

A molecular roadmap to the plant immune system.
Bentham et al. (2020)
2 more