6WIC

Pre-catalytic quaternary complex of human Polymerase Mu on a complementary DNA double-strand break substrate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report



Literature

Structural snapshots of human DNA polymerase mu engaged on a DNA double-strand break.

Kaminski, A.M.Pryor, J.M.Ramsden, D.A.Kunkel, T.A.Pedersen, L.C.Bebenek, K.

(2020) Nat Commun 11: 4784-4784

  • DOI: 10.1038/s41467-020-18506-5
  • Primary Citation of Related Structures:  
    6WIC, 6WIE, 6WID

  • PubMed Abstract: 
  • 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 th ...

    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.


    Organizational Affiliation

    Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, 111 TW Alexander Dr., Bldg. 101/Rm F338, Research Triangle Park, NC, 27709, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed DNA/RNA polymerase muA356Homo sapiensMutation(s): 0 
Gene Names: POLMpolmu
EC: 2.7.7.7
Find proteins for Q9NP87 (Homo sapiens)
Explore Q9NP87 
Go to UniProtKB:  Q9NP87
NIH Common Fund Data Resources
PHAROS  Q9NP87
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*GP*CP*AP*T)-3')T6synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*AP*CP*G)-3')U3synthetic construct
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        DNA (5'-D(*CP*GP*TP*A)-3')P4synthetic construct
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        • Entity ID: 5
          MoleculeChainsLengthOrganismImage
          DNA (5'-D(P*GP*CP*CP*G)-3')D4synthetic construct
          Small Molecules
          Ligands 8 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          DUP
          Query on DUP

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          A
          2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE
          C9 H16 N3 O13 P3
          XZLLMTSKYYYJLH-SHYZEUOFSA-N
           Ligand Interaction
          1PE
          Query on 1PE

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          A
          PENTAETHYLENE GLYCOL
          C10 H22 O6
          JLFNLZLINWHATN-UHFFFAOYSA-N
           Ligand Interaction
          PEG
          Query on PEG

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          A
          DI(HYDROXYETHYL)ETHER
          C4 H10 O3
          MTHSVFCYNBDYFN-UHFFFAOYSA-N
           Ligand Interaction
          GOL
          Query on GOL

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          A
          GLYCEROL
          C3 H8 O3
          PEDCQBHIVMGVHV-UHFFFAOYSA-N
           Ligand Interaction
          K
          Query on K

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          A
          POTASSIUM ION
          K
          NPYPAHLBTDXSSS-UHFFFAOYSA-N
           Ligand Interaction
          CL
          Query on CL

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          A
          CHLORIDE ION
          Cl
          VEXZGXHMUGYJMC-UHFFFAOYSA-M
           Ligand Interaction
          MG
          Query on MG

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          A
          MAGNESIUM ION
          Mg
          JLVVSXFLKOJNIY-UHFFFAOYSA-N
           Ligand Interaction
          NA
          Query on NA

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          A
          SODIUM ION
          Na
          FKNQFGJONOIPTF-UHFFFAOYSA-N
           Ligand Interaction
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 1.55 Å
          • R-Value Free: 0.179 
          • R-Value Work: 0.166 
          • R-Value Observed: 0.166 
          • Space Group: P 21 21 21
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 60.134α = 90
          b = 62.233β = 90
          c = 118.054γ = 90
          Software Package:
          Software NamePurpose
          PHENIXrefinement
          HKL-2000data reduction
          HKL-2000data scaling
          PHASERphasing

          Structure Validation

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          Entry History & Funding Information

          Deposition Data


          Funding OrganizationLocationGrant Number
          National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States1ZIA ES 102645
          National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United StatesZ01 ES065070

          Revision History 

          • Version 1.0: 2020-10-07
            Type: Initial release