› 1p8k

X-ray diffraction
2.6Å resolution

The structure and DNA recognition of a bifunctional homing endonuclease and group I intron splicing factor

Released:
DOI: 10.2210/pdb1p8k/pdb
PDB entry 1p8k coloured by chain, front view.
PDB entry 1p8k coloured by chain, side view.
PDB entry 1p8k coloured by chain, top view.
Source organism: Aspergillus nidulans
Primary publication:
Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor.
Bolduc JM, Spiegel PC, Chatterjee P, Brady KL, Downing ME, Caprara MG, Waring RB, Stoddard BL
Genes Dev 17 2875-88 (2003)
PMID: 14633971

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114366 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
Truncated non-functional cytochrome b Chain: Z
Molecule details ›
Chain: Z
Length: 254 amino acids
Theoretical weight: 29.62 KDa
Source organism: Aspergillus nidulans
Expression system: Escherichia coli
UniProt:
  • Canonical: P03880 (Residues: 237-488; Coverage: 52%)
Gene name: I-AniI
Sequence domains: LAGLIDADG endonuclease
Structure domains: Homing endonucleases
5'-D(P*GP*CP*GP*CP*GP*CP*TP*GP*AP*GP*GP*AP*GP*GP*TP*TP*TP*C)-3' Chain: A
Molecule details ›
Chain: A
Length: 18 nucleotides
Theoretical weight: 5.59 KDa
Source organism: Aspergillus nidulans
Expression system: Not provided
5'-D(P*TP*CP*TP*GP*TP*AP*AP*AP*GP*CP*GP*CP*A)-3' Chain: B
Molecule details ›
Chain: B
Length: 13 nucleotides
Theoretical weight: 3.98 KDa
Source organism: Aspergillus nidulans
Expression system: Not provided
5'-D(P*GP*CP*GP*CP*TP*TP*TP*AP*CP*AP*GP*AP*GP*AP*AP*A)-3' Chain: C
Molecule details ›
Chain: C
Length: 16 nucleotides
Theoretical weight: 4.93 KDa
Source organism: Aspergillus nidulans
Expression system: Not provided
5'-D(P*CP*CP*TP*CP*CP*TP*CP*AP*GP*CP*GP*CP*GP*CP*T)-3' Chain: D
Molecule details ›
Chain: D
Length: 15 nucleotides
Theoretical weight: 4.48 KDa
Source organism: Aspergillus nidulans
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand MG 2 x MG
1 modified residue:
Ligand MSE 2 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P21
Unit cell:
a: 60.462Å b: 72.841Å c: 65.231Å
α: 90° β: 108.21° γ: 90°
R-values:
R R work R free
0.247 0.239 0.264
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

12 review citations

Homing endonucleases: from microbial genetic invaders to reagents for targeted DNA modification.
Stoddard BL. (2011)
11 more

3 mentions without citation

Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor.
Bolduc et al. (2003)
2 more