› 5jgh

X-ray diffraction
2.6Å resolution

Crystal structure of the mitochondrial DNA packaging protein Abf2p in complex with DNA at 2.6 Angstrom resolution

Released:
DOI: 10.2210/pdb5jgh/pdb
PDB entry 5jgh coloured by chain, front view.
PDB entry 5jgh coloured by chain, side view.
PDB entry 5jgh 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-118869 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
ARS-binding factor 2, mitochondrial Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
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(*TP*TP*TP*AP*TP*TP*AP*TP*TP*TP*TP*AP*TP*AP*TP*TP*AP*TP*AP*TP*AP*A)-3') Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 22 nucleotides
Theoretical weight: 6.72 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided
DNA (5'-D(*TP*TP*AP*TP*AP*TP*AP*AP*TP*AP*TP*AP*AP*AP*AP*TP*AP*AP*TP*AP*AP*A)-3') Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 22 nucleotides
Theoretical weight: 6.77 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand ACT 2 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P21
Unit cell:
a: 71.989Å b: 131.991Å c: 71.994Å
α: 90° β: 103.21° γ: 90°
R-values:
R R work R free
0.228 0.227 0.26
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

4 review citations

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

2 mentions without citation

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