4X0P

Ternary complex of human DNA polymerase theta C-terminal domain binding ddATP opposite a tetrahydrofuran AP site analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.91 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Human DNA polymerase theta grasps the primer terminus to mediate DNA repair.

Zahn, K.E.Averill, A.M.Aller, P.Wood, R.D.Doublie, S.

(2015) Nat Struct Mol Biol 22: 304-311

  • DOI: https://doi.org/10.1038/nsmb.2993
  • Primary Citation of Related Structures:  
    4X0P, 4X0Q

  • PubMed Abstract: 

    DNA polymerase θ protects against genomic instability via an alternative end-joining repair pathway for DNA double-strand breaks. Polymerase θ is overexpressed in breast, lung and oral cancers, and reduction of its activity in mammalian cells increases sensitivity to double-strand break-inducing agents, including ionizing radiation. Reported here are crystal structures of the C-terminal polymerase domain from human polymerase θ, illustrating two potential modes of dimerization. One structure depicts insertion of ddATP opposite an abasic-site analog during translesion DNA synthesis. The second structure describes a cognate ddGTP complex. Polymerase θ uses a specialized thumb subdomain to establish unique upstream contacts to the primer DNA strand, including an interaction with the 3'-terminal phosphate from one of five distinctive insertion loops. These observations demonstrate how polymerase θ grasps the primer to bypass DNA lesions or extend poorly annealed DNA termini to mediate end-joining.


  • Organizational Affiliation

    Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA polymerase theta
A, B, C, D
799Homo sapiensMutation(s): 0 
Gene Names: POLQPOLH
EC: 2.7.7.7 (PDB Primary Data), 3.6.4.12 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75417 (Homo sapiens)
Explore O75417 
Go to UniProtKB:  O75417
PHAROS:  O75417
GTEx:  ENSG00000051341 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75417
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*C)-3')E [auth F],
G [auth H],
I [auth J],
K [auth L]
13synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*TP*TP*GP*AP*AP*TP*GP*AP*CP*AP*GP*CP*CP*GP*CP*G)-3')F [auth E],
H [auth G],
J [auth I],
L [auth K]
18synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DDS
Query on DDS

Download Ideal Coordinates CCD File 
BA [auth D],
P [auth A],
T [auth B],
X [auth C]
2',3'-dideoxyadenosine triphosphate
C10 H16 N5 O11 P3
OAKPWEUQDVLTCN-NKWVEPMBSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
M [auth A]
N [auth A]
Q [auth B]
R [auth B]
U [auth C]
M [auth A],
N [auth A],
Q [auth B],
R [auth B],
U [auth C],
V [auth C],
Y [auth D],
Z [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth D],
O [auth A],
S [auth B],
W [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.91 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.241 
  • R-Value Observed: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126.921α = 90
b = 136.971β = 90
c = 247.991γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01CA052040

Revision History  (Full details and data files)

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2015-04-01
    Changes: Database references
  • Version 1.2: 2015-04-15
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Derived calculations, Source and taxonomy
  • Version 1.4: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description