› 6fb5

X-ray diffraction
2.2Å resolution

Crystal Structure of a Tailored I-CreI Homing Endonuclease Protein (3115 variant) in complex with an altered version of its target DNA (Haemoglobin beta subunit gene) at 5NNN region in the presence of Magnesium

Released:
DOI: 10.2210/pdb6fb5/pdb
PDB entry 6fb5 coloured by chain, front view.
PDB entry 6fb5 coloured by chain, side view.
PDB entry 6fb5 coloured by chain, top view.
Source organism: Chlamydomonas reinhardtii
Primary publication:
Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.
Prieto J, Redondo P, López-Méndez B, D'Abramo M, Merino N, Blanco FJ, Duchateau P, Montoya G, Molina R
Sci Rep 8 10286 (2018)
PMID: 29980759

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119886 (preferred)
Entry contents:
2 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (4 distinct):
DNA endonuclease I-CreI Chain: A
Molecule details ›
Chain: A
Length: 153 amino acids
Theoretical weight: 17.53 KDa
Source organism: Chlamydomonas reinhardtii
Expression system: Escherichia coli
UniProt:
  • Canonical: P05725 (Residues: 2-154; Coverage: 94%)
Sequence domains: LAGLIDADG endonuclease
Structure domains: Homing endonucleases
DNA endonuclease I-CreI Chain: B
Molecule details ›
Chain: B
Length: 154 amino acids
Theoretical weight: 17.58 KDa
Source organism: Chlamydomonas reinhardtii
Expression system: Escherichia coli
UniProt:
  • Canonical: P05725 (Residues: 2-155; Coverage: 95%)
Sequence domains: LAGLIDADG endonuclease
Structure domains: Homing endonucleases
DNA (5'-D(*TP*CP*AP*GP*AP*CP*TP*TP*GP*TP*CP*CP*AP*CP*AP*GP*GP*AP*GP*TP*CP*AP*GP*A)-3') Chain: D
Molecule details ›
Chain: D
Length: 24 nucleotides
Theoretical weight: 7.38 KDa
DNA (5'-D(*TP*CP*TP*GP*AP*CP*TP*CP*CP*TP*GP*TP*GP*GP*AP*CP*AP*AP*GP*TP*CP*TP*GP*A)-3') Chain: F
Molecule details ›
Chain: F
Length: 24 nucleotides
Theoretical weight: 7.36 KDa

Ligands and Environments

3 bound ligands:
Ligand MG 4 x MG
Ligand ACT 1 x ACT
Ligand PGO 1 x PGO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: P21
Unit cell:
a: 45.29Å b: 68.005Å c: 83.03Å
α: 90° β: 96.55° γ: 90°
R-values:
R R work R free
0.191 0.189 0.219
Expression system: Escherichia coli

Quick links

Citations

7 review citations

The genome editing revolution: review.
Khalil AM. (2020)
6 more

1 mention without citation

Dissecting and predicting different types of binding sites in nucleic acids based on structural information.
Jiang et al. (2022)