6XBU | pdb_00006xbu

polymerase domain of polymerase-theta


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 
    0.281 (Depositor), 0.286 (DCC) 
  • R-Value Work: 
    0.250 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 
    0.253 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Pol theta reverse transcribes RNA and promotes RNA-templated DNA repair.

Chandramouly, G.Zhao, J.McDevitt, S.Rusanov, T.Hoang, T.Borisonnik, N.Treddinick, T.Lopezcolorado, F.W.Kent, T.Siddique, L.A.Mallon, J.Huhn, J.Shoda, Z.Kashkina, E.Brambati, A.Stark, J.M.Chen, X.S.Pomerantz, R.T.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abf1771
  • Primary Citation Related Structures: 
    6XBU

  • PubMed Abstract: 

    Genome-embedded ribonucleotides arrest replicative DNA polymerases (Pols) and cause DNA breaks. Whether mammalian DNA repair Pols efficiently use template ribonucleotides and promote RNA-templated DNA repair synthesis remains unknown. We find that human Polθ reverse transcribes RNA, similar to retroviral reverse transcriptases (RTs). Polθ exhibits a significantly higher velocity and fidelity of deoxyribonucleotide incorporation on RNA versus DNA. The 3.2-Å crystal structure of Polθ on a DNA/RNA primer-template with bound deoxyribonucleotide reveals that the enzyme undergoes a major structural transformation within the thumb subdomain to accommodate A-form DNA/RNA and forms multiple hydrogen bonds with template ribose 2'-hydroxyl groups like retroviral RTs. Last, we find that Polθ promotes RNA-templated DNA repair in mammalian cells. These findings suggest that Polθ was selected to accommodate template ribonucleotides during DNA repair.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.

Macromolecule Content 

  • Total Structure Weight: 82.48 kDa 
  • Atom Count: 5,118 
  • Modeled Residue Count: 620 
  • Deposited Residue Count: 682 
  • Unique protein chains: 1
  • Unique nucleic acid chains: 2

Macromolecules


Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA polymerase theta652Homo 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
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(P*GP*TP*CP*AP*TP*TP*G)-3')B [auth F]13synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(P*CP*CP*AP*AP*UP*GP*A)-3')C [auth E]17synthetic construct
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DG3

Query on DG3



Download:Ideal Coordinates CCD File
D [auth A]2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O12 P3
HDRRAMINWIWTNU-NTSWFWBYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free:  0.281 (Depositor), 0.286 (DCC) 
  • R-Value Work:  0.250 (Depositor), 0.252 (DCC) 
  • R-Value Observed: 0.253 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.52α = 90
b = 99.52β = 90
c = 193.15γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
PROCORdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM130889
Tower Cancer Research FoundationUnited States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM137124

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-09-22
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description