› 5jh0

X-ray diffraction
2.18Å resolution

Crystal structure of the mitochondrial DNA packaging protein Abf2p in complex with DNA at 2.18 Angstrom resolution

Released:
DOI: 10.2210/pdb5jh0/pdb
PDB entry 5jh0 coloured by chain, front view.
PDB entry 5jh0 coloured by chain, side view.
PDB entry 5jh0 coloured by chain, top view.
Source organisms:
Primary publication:
DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p.
Chakraborty A, Lyonnais S, Battistini F, Hospital A, Medici G, Prohens R, Orozco M, Vilardell J, Solà M
Nucleic Acids Res 45 951-967 (2017)
PMID: 27899643

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-118870 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
ARS-binding factor 2, mitochondrial Chains: A, D
Molecule details ›
Chains: A, D
Length: 163 amino acids
Theoretical weight: 19.49 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q02486 (Residues: 27-183; Coverage: 86%)
Gene names: ABF2, HIM1, YM9916.11, YMR072W
Sequence domains: HMG (high mobility group) box
DNA (5'-D(*AP*AP*TP*AP*AP*TP*AP*AP*AP*TP*TP*AP*TP*AP*TP*AP*AP*TP*AP*TP*AP*A)-3') Chains: B, E
Molecule details ›
Chains: B, E
Length: 22 nucleotides
Theoretical weight: 6.77 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
DNA (5'-D(*TP*TP*AP*TP*AP*TP*TP*AP*TP*AP*TP*AP*AP*TP*TP*TP*AP*TP*TP*AP*TP*T)-3') Chains: C, F
Molecule details ›
Chains: C, F
Length: 22 nucleotides
Theoretical weight: 6.72 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: C2
Unit cell:
a: 88.49Å b: 113.41Å c: 67.71Å
α: 90° β: 103.8° γ: 90°
R-values:
R R work R free
0.211 0.209 0.236
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

3 review citations

Structure, mechanism, and regulation of mitochondrial DNA transcription initiation.
Basu et al. (2020)
2 more

8 mentions without citation

Studying protein-DNA interactions using atomic force microscopy.
Beckwitt et al. (2018)
7 more