› 7ji8

X-ray diffraction
2.95Å resolution

Self-assembly of a 3D DNA crystal lattice (4x6 scramble junction version) containing the J31 immobile Holliday junction with R3 symmetry

Released:
DOI: 10.2210/pdb7ji8/pdb
PDB entry 7ji8 coloured by chain, front view.
PDB entry 7ji8 coloured by chain, side view.
PDB entry 7ji8 coloured by chain, top view.
Source organism: synthetic construct
Primary publication:
The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly.
Simmons CR, MacCulloch T, Krepl M, Matthies M, Buchberger A, Crawford I, Šponer J, Šulc P, Stephanopoulos N, Yan H
OpenAccess logo Nat Commun 13 3112 (2022)
PMID: 35662248

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-121324 (preferred)
Entry contents:
4 distinct DNA molecules
Macromolecules (4 distinct):
DNA (5'-D(*GP*AP*AP*CP*GP*AP*CP*AP*CP*AP*GP*A)-3') Chain: A
Molecule details ›
Chain: A
Length: 12 nucleotides
Theoretical weight: 3.69 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*CP*GP*GP*CP*GP*AP*CP*TP*C)-3') Chain: B
Molecule details ›
Chain: B
Length: 9 nucleotides
Theoretical weight: 2.72 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(P*TP*CP*TP*CP*CP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 6 nucleotides
Theoretical weight: 1.76 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*GP*GP*TP*GP*TP*CP*GP*T)-3') Chain: D
Molecule details ›
Chain: D
Length: 15 nucleotides
Theoretical weight: 4.63 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CAC 1 x CAC
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-ID
Spacegroup: R3
Unit cell:
a: 113.109Å b: 113.109Å c: 50.385Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.257 0.255 0.281
Expression system: Not provided

Quick links

Citations

4 review citations

The development of nucleic acids force fields: From an unchallenged past to a competitive future.
Liebl et al. (2023)
3 more