› 6go7

X-ray diffraction
2.55Å resolution

TdT chimera (Loop1 of pol mu) - full DNA synapsis complex

Released:
DOI: 10.2210/pdb6go7/pdb
PDB entry 6go7 coloured by chain, front view.
PDB entry 6go7 coloured by chain, side view.
PDB entry 6go7 coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Structural evidence for an in trans base selection mechanism involving Loop1 in polymerase μ at an NHEJ double-strand break junction.
Loc'h J, Gerodimos CA, Rosario S, Tekpinar M, Lieber MR, Delarue M
J Biol Chem 294 10579-10595 (2019)
PMID: 31138645

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119964 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
DNA nucleotidylexotransferase; DNA-directed DNA/RNA polymerase mu Chain: A
Molecule details ›
Chain: A
Length: 401 amino acids
Theoretical weight: 45.85 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: P09838 (Residues: 132-377, 409-510; Coverage: 68%)
  • Canonical: Q9JIW4 (Residues: 363-394; Coverage: 7%)
Gene names: Dntt, Polm, Tdt, polmu
Sequence domains:
DNA (5'-D(*AP*AP*AP*AP*AP*C)-3') Chains: F, G
Molecule details ›
Chains: F, G
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
DNA (5'-D(*TP*TP*TP*TP*TP*GP*C)-3') Chains: E, H, I, J
Molecule details ›
Chains: E, H, I, J
Length: 7 nucleotides
Theoretical weight: 2.09 KDa

Ligands and Environments

3 bound ligands:
Ligand NA 1 x NA
Ligand DCT 1 x DCT
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID23-2
Spacegroup: P21
Unit cell:
a: 47Å b: 90.31Å c: 65.9Å
α: 90° β: 106.79° γ: 90°
R-values:
R R work R free
0.192 0.191 0.222
Expression system: Escherichia coli

Quick links

Citations

2 review citations

The molecular basis and disease relevance of non-homologous DNA end joining.
Zhao et al. (2020)
1 more

3 mentions without citation

Polymerase μ in non-homologous DNA end joining: importance of the order of arrival at a double-strand break in a purified system.
Zhao et al. (2020)
2 more