› 6wid

X-ray diffraction
1.5Å resolution

Nucleotide incorporation intermediate into quaternary complex of human Polymerase Mu on a complementary DNA double-strand break substrate

Released:
DOI: 10.2210/pdb6wid/pdb
PDB entry 6wid coloured by chain, front view.
PDB entry 6wid coloured by chain, side view.
PDB entry 6wid coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural snapshots of human DNA polymerase μ engaged on a DNA double-strand break.
Kaminski AM, Pryor JM, Ramsden DA, Kunkel TA, Pedersen LC, Bebenek K
Nat Commun 11 4784 (2020)
PMID: 32963245

Function and Biology Details

Reaction catalysed: 
Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120842 (preferred)
Entry contents:
1 distinct polypeptide molecule
4 distinct DNA molecules
Macromolecules (5 distinct):
DNA-directed DNA/RNA polymerase mu Chain: A
Molecule details ›
Chain: A
Length: 356 amino acids
Theoretical weight: 40.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9NP87 (Residues: 132-397, 411-494; Coverage: 71%)
Gene names: POLM, polmu
Sequence domains:
DNA (5'-D(*CP*GP*GP*CP*AP*T)-3') Chain: T
Molecule details ›
Chain: T
Length: 6 nucleotides
Theoretical weight: 1.81 KDa
DNA (5'-D(*AP*CP*G)-3') Chain: U
Molecule details ›
Chain: U
Length: 3 nucleotides
Theoretical weight: 887 Da
DNA (5'-D(*CP*GP*TP*AP*T)-3') Chain: P
Molecule details ›
Chain: P
Length: 5 nucleotides
Theoretical weight: 1.5 KDa
DNA (5'-D(P*GP*CP*CP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 4 nucleotides
Theoretical weight: 1.19 KDa

Ligands and Environments

8 bound ligands:
Ligand DUP 1 x DUP
Ligand PPV 1 x PPV
Ligand MG 2 x MG
Ligand NA 1 x NA
Ligand CL 1 x CL
Ligand 1PE 1 x 1PE
Ligand GOL 2 x GOL
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P212121
Unit cell:
a: 60.186Å b: 62.04Å c: 118.32Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.164 0.164 0.177
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

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

3 mentions without citation

Structural snapshots of human DNA polymerase μ engaged on a DNA double-strand break.
Kaminski et al. (2020)
2 more