7COD | pdb_00007cod

Post insertion complex of DNA polymerase Mu (K438A/Q441A) with 1-nt gapped DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.211 (Depositor), 0.213 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 
    0.187 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7COD

This is version 1.1 of the entry. See complete history

Literature

Mechanism of genome instability mediated by human DNA polymerase mu misincorporation.

Guo, M.Wang, Y.Tang, Y.Chen, Z.Hou, J.Dai, J.Wang, Y.Wang, L.Xu, H.Tian, B.Hua, Y.Zhao, Y.

(2021) Nat Commun 12: 3759-3759

  • DOI: https://doi.org/10.1038/s41467-021-24096-7
  • Primary Citation Related Structures: 
    7CO6, 7CO8, 7CO9, 7COA, 7COB, 7COC, 7COD

  • PubMed Abstract: 

    Pol μ is capable of performing gap-filling repair synthesis in the nonhomologous end joining (NHEJ) pathway. Together with DNA ligase, misincorporation of dGTP opposite the templating T by Pol μ results in a promutagenic T:G mispair, leading to genomic instability. Here, crystal structures and kinetics of Pol μ substituting dGTP for dATP on gapped DNA substrates containing templating T were determined and compared. Pol μ is highly mutagenic on a 2-nt gapped DNA substrate, with T:dGTP base pairing at the 3' end of the gap. Two residues (Lys438 and Gln441) interact with T:dGTP and fine tune the active site microenvironments. The in-crystal misincorporation reaction of Pol μ revealed an unexpected second dGTP in the active site, suggesting its potential mutagenic role among human X family polymerases in NHEJ.


  • Organizational Affiliation
    • Institute of Biophysics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.

Macromolecule Content 

  • Total Structure Weight: 59.82 kDa 
  • Atom Count: 3,531 
  • Modeled Residue Count: 346 
  • Deposited Residue Count: 500 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 3

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA-directed DNA/RNA polymerase mu482Homo sapiensMutation(s): 3 
Gene Names: POLMpolmu
EC: 2.7.7.7
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NP87 (Homo sapiens)
Explore Q9NP87 
Go to UniProtKB:  Q9NP87
PHAROS:  Q9NP87
GTEx:  ENSG00000122678 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NP87
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*GP*CP*TP*TP*AP*CP*G)-3')B [auth T]9synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*TP*AP*G)-3')C [auth P]5synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 4
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*CP*CP*G)-3')4synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGT
(Subject of Investigation/LOI)

Query on DGT



Download:Ideal Coordinates CCD File
F [auth A]2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
HAAZLUGHYHWQIW-KVQBGUIXSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
H [auth A],
J [auth P]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
I [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.211 (Depositor), 0.213 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.187 (DCC) 
  • R-Value Observed: 0.187 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.18α = 90
b = 68.52β = 90
c = 111.91γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31670819

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description