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- PDB-6xbu: polymerase domain of polymerase-theta -

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Basic information

Entry
Database: PDB / ID: 6xbu
Titlepolymerase domain of polymerase-theta
Components
  • DNA (5'-D(P*GP*TP*CP*AP*TP*TP*G)-3')
  • DNA polymerase thetaPOLQ
  • RNA (5'-R(P*CP*CP*AP*AP*UP*GP*A)-3')
KeywordsDNA BINDING PROTEIN/DNA/RNA / Replication / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA-RNA complex
Function / homology
Function and homology information


single-stranded DNA endodeoxyribonuclease activity / double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / negative regulation of double-strand break repair via homologous recombination / replication fork processing / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / error-prone translesion synthesis ...single-stranded DNA endodeoxyribonuclease activity / double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / negative regulation of double-strand break repair via homologous recombination / replication fork processing / site of DNA damage / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / error-prone translesion synthesis / DNA helicase activity / base-excision repair / protein homooligomerization / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / double-strand break repair / site of double-strand break / DNA helicase / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / chromatin binding / Golgi apparatus / magnesium ion binding / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / cytosol
Similarity search - Function
DNA polymerase theta-like, helix-turn-helix domain / : / Helix-turn-helix domain / DNA_pol_Q helicase like region helical domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain ...DNA polymerase theta-like, helix-turn-helix domain / : / Helix-turn-helix domain / DNA_pol_Q helicase like region helical domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. / DNA-directed DNA polymerase, family A, palm domain / DNA polymerase A domain / DEAD/DEAH box helicase / DEAD/DEAH box helicase domain / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / RNA / RNA (> 10) / DNA polymerase theta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.29 Å
AuthorsChen, X. / Pomerantz, R. / Zhao, J.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM130889 United States
Tower Cancer Research Foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM137124 United States
CitationJournal: Sci Adv / Year: 2021
Title: Pol theta reverse transcribes RNA and promotes RNA-templated DNA repair.
Authors: 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. / ...Authors: 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.
History
DepositionJun 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase theta
F: DNA (5'-D(P*GP*TP*CP*AP*TP*TP*G)-3')
E: RNA (5'-R(P*CP*CP*AP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4834
Polymers81,9923
Non-polymers4911
Water0
1
A: DNA polymerase theta
F: DNA (5'-D(P*GP*TP*CP*AP*TP*TP*G)-3')
E: RNA (5'-R(P*CP*CP*AP*AP*UP*GP*A)-3')
hetero molecules

A: DNA polymerase theta
F: DNA (5'-D(P*GP*TP*CP*AP*TP*TP*G)-3')
E: RNA (5'-R(P*CP*CP*AP*AP*UP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,9668
Polymers163,9836
Non-polymers9822
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area11170 Å2
ΔGint-39 kcal/mol
Surface area58290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.520, 99.520, 193.150
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein DNA polymerase theta / POLQ / DNA polymerase eta


Mass: 72591.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLQ, POLH / Production host: Escherichia coli (E. coli) / References: UniProt: O75417, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(P*GP*TP*CP*AP*TP*TP*G)-3')


Mass: 3998.595 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: RNA chain RNA (5'-R(P*CP*CP*AP*AP*UP*GP*A)-3')


Mass: 5401.292 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 67.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 20% (w/v) Ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 21, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 3.2→49.77 Å / Num. obs: 32393 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 108.63 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.304 / Net I/σ(I): 9.5
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 13.2 % / Rmerge(I) obs: 3.251 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1847 / CC1/2: 0.695 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.12-2829refinement
XDSdata reduction
PHASER2.8.0phasing
PDB_EXTRACT3.25data extraction
PROCORdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X0Q

4x0q


Resolution: 3.29→49.76 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 35.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2807 2171 6.7 %
Rwork0.2504 30222 -
obs0.2526 32393 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 228.76 Å2 / Biso mean: 121.0832 Å2 / Biso min: 64.38 Å2
Refinement stepCycle: final / Resolution: 3.29→49.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4778 312 30 0 5120
Biso mean--143.62 --
Num. residues----620
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145240
X-RAY DIFFRACTIONf_angle_d1.7637134
X-RAY DIFFRACTIONf_chiral_restr0.089807
X-RAY DIFFRACTIONf_plane_restr0.004853
X-RAY DIFFRACTIONf_dihedral_angle_d22.2571980
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2902-3.36170.38511380.3821877100
3.3617-3.43990.43631460.3656193099
3.4399-3.52590.38241340.37831845100
3.5259-3.62120.36051380.3316187299
3.6212-3.72770.35731340.29991879100
3.7277-3.8480.27161260.26811924100
3.848-3.98540.30641340.27011916100
3.9854-4.14490.27541370.275184699
4.1449-4.33350.24311320.24711920100
4.3335-4.56180.26581340.22161854100
4.5618-4.84740.27761300.21931893100
4.8474-5.22130.31341280.22671921100
5.2213-5.7460.31011380.25341878100
5.746-6.57590.28981500.27561905100
6.5759-8.27870.22391340.23961873100
8.2787-49.760.23111380.20111889100

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