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Entry Detail
PDB ID:
6WIC
Keywords:
TRANSFERASE/DNA
Title:
Pre-catalytic quaternary complex of human Polymerase Mu on a complementary DNA double-strand break substrate
Biological Source:
Source Organism:
Homo sapiens, synthetic construct
Host Organism:
Escherichia coli BL21(DE3)
PDB Version:
Deposition Date:
2020-04-09
Release Date:
2020-10-07
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
1.55 Å
R-Value Free:
0.17
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 21 21 21
6WIC validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Description:DNA-directed DNA/RNA polymerase mu
Mutations:P398-P410 deletion replaced by G410 linker
Chain IDs:A
Chain Length:356
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NP87 Pfam ID:PF14716, PF10391, PF14792, PF14791 EC:2.7.7.7
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(P*GP*CP*CP*G)-3')
Chain IDs:E (auth: D)
Chain Length:4
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*CP*GP*TP*A)-3')
Chain IDs:D (auth: P)
Chain Length:4
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*CP*GP*GP*CP*AP*T)-3')
Chain IDs:B (auth: T)
Chain Length:6
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Description:DNA (5'-D(*AP*CP*G)-3')
Chain IDs:C (auth: U)
Chain Length:3
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
1PE
CL
DUP
GOL
K
MG
NA
PEG
Primary Citation
Structural snapshots of human DNA polymerase mu engaged on a DNA double-strand break.
Nat Commun 11 4784 4784 (2020)
PMID: 32963245 DOI: 10.1038/s41467-020-18506-5

Abstact

Genomic integrity is threatened by cytotoxic DNA double-strand breaks (DSBs), which must be resolved efficiently to prevent sequence loss, chromosomal rearrangements/translocations, or cell death. Polymerase μ (Polμ) participates in DSB repair via the nonhomologous end-joining (NHEJ) pathway, by filling small sequence gaps in broken ends to create substrates ultimately ligatable by DNA Ligase IV. Here we present structures of human Polμ engaging a DSB substrate. Synapsis is mediated solely by Polμ, facilitated by single-nucleotide homology at the break site, wherein both ends of the discontinuous template strand are stabilized by a hydrogen bonding network. The active site in the quaternary Pol μ complex is poised for catalysis and nucleotide incoporation proceeds in crystallo. These structures demonstrate that Polμ may address complementary DSB substrates during NHEJ in a manner indistinguishable from single-strand breaks.

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Primary Citation of related structures
6WIC