› 6ltu

X-ray diffraction
2.57Å resolution

Crystal structure of Cas12i2 ternary complex with double Mg2+ bound in catalytic pocket

Released:
DOI: 10.2210/pdb6ltu/pdb
PDB entry 6ltu coloured by chain, front view.
PDB entry 6ltu coloured by chain, side view.
PDB entry 6ltu coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2.
Huang X, Sun W, Cheng Z, Chen M, Li X, Wang J, Sheng G, Gong W, Wang Y
OpenAccess logo Nat Commun 11 5241 (2020)
PMID: 33067443

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
PDBe Complex ID:
PDB-CPX-120228 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
1 distinct RNA molecule
Macromolecules (5 distinct):
Cas12i2 Chain: A
Molecule details ›
Chain: A
Length: 1055 amino acids
Theoretical weight: 121.47 KDa
Source organism: unidentified
Expression system: Escherichia coli 'BL21-Gold(DE3)pLysS AG'
DNA (5'-D(*GP*CP*CP*GP*CP*TP*TP*TP*CP*TP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.6 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (35-MER) Chain: C
Molecule details ›
Chain: C
Length: 35 nucleotides
Theoretical weight: 10.74 KDa
Source organism: synthetic construct
Expression system: Not provided
trans ssDNA Chain: E
Molecule details ›
Chain: E
Length: 5 nucleotides
Theoretical weight: 1.46 KDa
Source organism: synthetic construct
Expression system: Not provided
RNA (56-mer) Chain: B
Molecule details ›
Chain: B
Length: 58 nucleotides
Theoretical weight: 18.66 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand MG 3 x MG
Ligand EDO 1 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: C2221
Unit cell:
a: 94.329Å b: 123.575Å c: 281.218Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.202 0.229
Expression systems:
  • Escherichia coli 'BL21-Gold(DE3)pLysS AG'
  • Not provided

Quick links

Citations

2 review citations

Structural biology of CRISPR-Cas immunity and genome editing enzymes.
Wang et al. (2022)
1 more

2 mentions without citation

Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2.
Huang et al. (2020)
1 more