› 5tyf

X-ray diffraction
1.97Å resolution

DNA Polymerase Mu Product Complex, 10 mM Mg2+ (270 min)

Released:
DOI: 10.2210/pdb5tyf/pdb
PDB entry 5tyf coloured by chain, front view.
PDB entry 5tyf coloured by chain, side view.
PDB entry 5tyf coloured by chain, top view.
Source organisms:
Primary publication:
Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.
Jamsen JA, Beard WA, Pedersen LC, Shock DD, Moon AF, Krahn JM, Bebenek K, Kunkel TA, Wilson SH
Nat Commun 8 253 (2017)
PMID: 28811466

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 tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-119173 (preferred)
Entry contents:
1 distinct polypeptide molecule
3 distinct DNA molecules
Macromolecules (4 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: 132-494; Coverage: 71%)
Gene names: POLM, polmu
Sequence domains:
Structure domains:
DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3') Chain: T
Molecule details ›
Chain: T
Length: 9 nucleotides
Theoretical weight: 2.74 KDa
Source organism: unidentified
Expression system: Not provided
DNA (5'-D(*CP*GP*TP*AP*T)-3') Chain: P
Molecule details ›
Chain: P
Length: 5 nucleotides
Theoretical weight: 1.5 KDa
Source organism: unidentified
Expression system: Not provided
DNA (5'-D(P*GP*CP*CP*G)-3') Chain: D
Molecule details ›
Chain: D
Length: 4 nucleotides
Theoretical weight: 1.19 KDa
Source organism: unidentified
Expression system: Not provided

Ligands and Environments

6 bound ligands:
Ligand MG 1 x MG
Ligand NA 2 x NA
Ligand EDO 2 x EDO
Ligand EPE 1 x EPE
Ligand DTT 1 x DTT
Ligand GOA 1 x GOA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU MICROMAX-007 HF
Spacegroup: P212121
Unit cell:
a: 59.994Å b: 68.482Å c: 110.702Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.175 0.174 0.205
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

10 review citations

Structure and function relationships in mammalian DNA polymerases.
Hoitsma et al. (2020)
9 more

1 mention without citation

Time-lapse crystallography snapshots of a double-strand break repair polymerase in action.
Jamsen et al. (2017)