› 1u3e

X-ray diffraction
2.92Å resolution

DNA binding and cleavage by the HNH homing endonuclease I-HmuI

Released:
DOI: 10.2210/pdb1u3e/pdb
PDB entry 1u3e coloured by chain, front view.
PDB entry 1u3e coloured by chain, side view.
PDB entry 1u3e coloured by chain, top view.
Source organism: Okubovirus SPO1
Primary publication:
DNA binding and cleavage by the HNH homing endonuclease I-HmuI.
Shen BW, Landthaler M, Shub DA, Stoddard BL
J Mol Biol 342 43-56 (2004)
PMID: 15313606

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-114678 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 distinct):
DNA endonuclease I-HmuI Chain: M
Molecule details ›
Chain: M
Length: 174 amino acids
Theoretical weight: 19.8 KDa
Source organism: Bacillus virus SPO1
Expression system: Escherichia coli
UniProt:
  • Canonical: P34081 (Residues: 1-174; Coverage: 100%)
Sequence domains:
Structure domains:
36-MER Chain: A
Molecule details ›
Chain: A
Length: 36 nucleotides
Theoretical weight: 11.04 KDa
Source organism: Okubovirus SPO1
Expression system: Not provided
5'-D(*CP*TP*TP*AP*CP*GP*TP*GP*GP*GP*AP*AP*TP*TP*GP*CP*TP*GP*AP*GP*C)-3' Chain: B
Molecule details ›
Chain: B
Length: 21 nucleotides
Theoretical weight: 6.49 KDa
Source organism: Okubovirus SPO1
Expression system: Not provided
5'-D(P*GP*TP*TP*AP*GP*GP*CP*TP*CP*AP*TP*TP*AP*CP*T)-3' Chain: C
Molecule details ›
Chain: C
Length: 15 nucleotides
Theoretical weight: 4.57 KDa
Source organism: Okubovirus SPO1
Expression system: Not provided

Ligands and Environments

4 bound ligands:
Ligand SR 4 x SR
Ligand EDO 7 x EDO
Ligand MN 1 x MN
Ligand TRS 1 x TRS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2, ALS BEAMLINE 5.0.1
Spacegroup: I222
Unit cell:
a: 45Å b: 108.3Å c: 248.1Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.22 0.216 0.247
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

8 review citations

Origins of specificity in protein-DNA recognition.
Rohs et al. (2010)
7 more

11 mentions without citation

Structures of Cas9 endonucleases reveal RNA-mediated conformational activation.
Jinek et al. (2014)
10 more