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- PDB-9ysh: Allosteric inhibitor of human DNA polymerase theta -

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Basic information

Entry
Database: PDB / ID: 9ysh
TitleAllosteric inhibitor of human DNA polymerase theta
Components
  • DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*C)-3')
  • DNA (5'-D(*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
  • DNA polymerase theta
KeywordsDNA BINDING PROTEIN / TRANSFERASE/INHIBITOR / inhibitor / complex / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / DNA synthesis involved in DNA repair / replication fork processing / mitochondrial nucleoid / 5'-deoxyribose-5-phosphate lyase activity / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / somatic hypermutation of immunoglobulin genes ...double-strand break repair via alternative nonhomologous end joining / HDR through MMEJ (alt-NHEJ) / single-stranded DNA helicase activity / DNA synthesis involved in DNA repair / replication fork processing / mitochondrial nucleoid / 5'-deoxyribose-5-phosphate lyase activity / error-prone translesion synthesis / negative regulation of double-strand break repair via homologous recombination / somatic hypermutation of immunoglobulin genes / site of DNA damage / DNA helicase activity / protein homooligomerization / base-excision repair / RNA-directed DNA polymerase / RNA-directed DNA polymerase activity / double-strand break repair / site of double-strand break / DNA-directed DNA polymerase / DNA helicase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA repair / chromatin binding / DNA damage response / magnesium ion binding / Golgi apparatus / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
: / : / DNA_pol_Q helicase like region helical domain / Domain of unknown function (DUF7898) / DNA polymerase theta-like, helix-turn-helix domain / Helix-turn-helix domain / DNA polymerase A / DNA polymerase family A / DNA-directed DNA polymerase, family A, conserved site / DNA polymerase family A signature. ...: / : / DNA_pol_Q helicase like region helical domain / Domain of unknown function (DUF7898) / DNA polymerase theta-like, helix-turn-helix domain / Helix-turn-helix 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 domain / DEAD/DEAH box helicase / 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) / DNA polymerase theta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsMader, P. / Sicheri, F.
Funding support Canada, 5items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-143277 Canada
Canadian Institutes of Health Research (CIHR)PJT-178026 Canada
Canadian Institutes of Health Research (CIHR)PJT-186218 Canada
Canadian Institutes of Health Research (CIHR)PJT-180338 Canada
Other privateTFRI 1107-04 Canada
Citation
Journal: Acs Med.Chem.Lett. / Year: 2026
Title: Design of a Targeted Covalent Probe to Interrogate the DNA Polymerase Activity of Pol theta.
Authors: Bubenik, M. / Mader, P. / Orlicky, S. / Perryman, A.L. / Hamel, M. / Godbout, C. / Falgueyret, J.P. / Kurinov, I. / Wong, C. / Gingras, A.C. / Mamane, Y. / Zinda, M. / Morris, S.J. / ...Authors: Bubenik, M. / Mader, P. / Orlicky, S. / Perryman, A.L. / Hamel, M. / Godbout, C. / Falgueyret, J.P. / Kurinov, I. / Wong, C. / Gingras, A.C. / Mamane, Y. / Zinda, M. / Morris, S.J. / Gallant, M. / Sfeir, A. / Black, W.C. / Durocher, D. / Zimmermann, M. / Sicheri, F.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionOct 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)171,57816
Polymers168,7126
Non-polymers2,86610
Water2,378132
1
A: DNA polymerase theta
B: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*C)-3')
C: DNA (5'-D(*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0959
Polymers84,3563
Non-polymers1,7396
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-26 kcal/mol
Surface area29910 Å2
MethodPISA
2
D: DNA polymerase theta
E: DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*C)-3')
F: DNA (5'-D(*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4837
Polymers84,3563
Non-polymers1,1274
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-19 kcal/mol
Surface area30430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)249.130, 66.634, 151.939
Angle α, β, γ (deg.)90.000, 122.730, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AD

#1: Protein DNA polymerase theta / DNA polymerase eta


Mass: 75200.070 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: engineered construct, 5 surface loops are truncated, AA 1868-1888, 1921-1933, 2149-2172, 2264-2303, and 2516-2523
Source: (gene. exp.) Homo sapiens (human) / Gene: POLQ, POLH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75417, DNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA (5'-D(*CP*GP*TP*CP*CP*AP*AP*TP*GP*AP*CP*AP*GP*CP*C)-3')


Mass: 5157.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligonucleotide / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*GP*CP*TP*GP*TP*CP*AP*TP*TP*G)-3')


Mass: 3998.595 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: synthetic oligonucleotide / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 142 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DG3 / 2'-3'-DIDEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#6: Chemical ChemComp-A1CZX / N-(4-{2-[2,4-bis(trifluoromethyl)phenyl]-N-phenylacetamido}but-2-yn-1-yl)pyridine-3-carboxamide


Mass: 519.438 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H19F6N3O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.14 Å3/Da / Density % sol: 61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 14% PEG 3350, 200 mM sodium-potassium tartrate, 6% glycerol, 0.02% sucrose monolaurate, and 20 mM spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.706→65.51 Å / Num. obs: 199656 / % possible obs: 99.09 % / Redundancy: 3.5 % / Biso Wilson estimate: 67.73 Å2 / CC1/2: 0.934 / CC star: 0.983 / Rmerge(I) obs: 0.1184 / Rpim(I) all: 0.07424 / Rrim(I) all: 0.1401 / Net I/σ(I): 6.77
Reflection shellResolution: 2.706→2.75 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1.268 / Mean I/σ(I) obs: 0.91 / Num. unique obs: 9155 / CC1/2: 0.426 / CC star: 0.773 / Rpim(I) all: 0.8029 / Rrim(I) all: 1.505 / % possible all: 93.09

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.71→65.51 Å / SU ML: 0.4376 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.0372
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2513 2777 4.85 %
Rwork0.2198 54478 -
obs0.2213 57255 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 84.08 Å2
Refinement stepCycle: LAST / Resolution: 2.71→65.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9660 969 191 132 10952
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002511127
X-RAY DIFFRACTIONf_angle_d0.472915310
X-RAY DIFFRACTIONf_chiral_restr0.03751727
X-RAY DIFFRACTIONf_plane_restr0.00361797
X-RAY DIFFRACTIONf_dihedral_angle_d17.84034067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.750.43131140.43222566X-RAY DIFFRACTION93.09
2.75-2.80.39151350.37912723X-RAY DIFFRACTION99.13
2.8-2.860.35131370.33442683X-RAY DIFFRACTION99.19
2.86-2.920.33481440.30982661X-RAY DIFFRACTION98.01
2.92-2.980.33371440.30072684X-RAY DIFFRACTION99.44
2.98-3.050.28411510.28872725X-RAY DIFFRACTION99.76
3.05-3.120.34221550.26972683X-RAY DIFFRACTION99.68
3.12-3.210.29011620.24992698X-RAY DIFFRACTION99.27
3.21-3.30.3061470.25012759X-RAY DIFFRACTION99.62
3.3-3.410.29481230.26072710X-RAY DIFFRACTION99.68
3.41-3.530.31231550.27542700X-RAY DIFFRACTION99.62
3.53-3.670.29021370.22882747X-RAY DIFFRACTION99.93
3.67-3.840.24291240.19732718X-RAY DIFFRACTION99.58
3.84-4.040.21951240.19082765X-RAY DIFFRACTION99.45
4.04-4.30.21761330.18642722X-RAY DIFFRACTION98.82
4.3-4.630.18311370.17252761X-RAY DIFFRACTION99.66
4.63-5.090.21821580.16512737X-RAY DIFFRACTION99.76
5.09-5.830.26491120.20652787X-RAY DIFFRACTION99.79
5.83-7.340.22121490.22652787X-RAY DIFFRACTION99.49
7.34-65.510.2031360.18772862X-RAY DIFFRACTION98.81
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.56454488365-0.0701413851246-0.1589787247040.143213443901-0.1311754492970.150505586851-0.04843607887680.516782502057-0.311792556289-0.4046604947410.211038485857-0.222937143722-0.02127739834130.6772213210740.2068057556630.505175740722-0.04069626914650.06398236501410.637221393203-0.1523961331740.33972570215760.063277607-12.696700162816.4165683903
20.4885336741180.3368995874390.02529855316650.2550654306910.09380532682470.220206067042-0.0278280131070.247624389866-0.1013203603110.04276833890950.072870715467-0.005401695155180.01746187916590.4782536410450.0871529717150.422877317061-0.04199099335430.01372794174420.53010446878-0.1185089523220.3478306663752.1143102864-10.075016959822.8752570092
30.827642817764-0.960643106961-0.2180554315071.406707294790.287952559730.3791236819250.0282764341737-0.02199691242750.2000339893080.09660993861770.178856225421-0.110391027264-0.3327834435460.2874530023790.04794775986220.57154022188-0.08565120837060.06291461915780.384536195369-0.02511080897560.3615026834244.5246642110.886511991640.9135726231
40.621462737687-0.239387932125-0.399173322570.7342995914210.1084185160111.109187286520.0398302847028-0.0290874353439-0.02565644574560.221186224102-0.01109510143250.295172520395-0.08994110904760.03382841123040.0009780788231720.452858082421-0.06485385979870.06542536948870.230910785462-0.03425642764420.41788955425831.1135889993-1.0067457993848.8069135475
50.18261764559-0.154514361289-0.2054659808750.3363385351480.07259134214190.279700171546-0.0508641166444-0.2923034396380.4555429273630.360237496345-0.0460176020053-0.118174890207-0.1298717043290.2817455899530.1659335921210.827129729653-0.3059912021130.07334679128430.551902362818-0.105588769970.77687930655847.648413426314.472878203654.0388082005
60.5851269638440.583374497650.5026617732990.5908150657930.4462105216140.653167298934-0.159499968414-0.183948680827-0.4890404175460.253546771569-0.0449368356432-1.440810086560.2379373911680.3015214303890.03123142573320.543206084081-0.1450112632220.01073197793240.47304620691-0.02583902227661.00244283247.945274334617.376955647149.3999552647
71.33068374953-0.1244782063830.8783025486781.3492552929-0.1798013030061.331008067520.08499924335120.211439311291-0.01953832879850.0943823895799-0.165918093061-0.1292374304080.07888703605230.247021438705-0.01671966695680.386302780108-0.0589020813287-0.03519833213080.7164675035720.1812461615730.460504985781-39.564845193-24.569241634912.6634554367
80.736665526311-0.09807220714560.8460415855920.212527480372-0.08006299152050.9890540085340.4363632935770.9471465260210.3106003435750.180800528046-0.0363341951498-0.4015353273610.119763041439-0.03710722522510.141965059610.99349267442-0.1684874511450.004684267738971.317526829140.029051609980.89984655279512.2830534762-24.438786887222.4739119463
90.760943326137-0.4566580917780.2409540707680.4704902716-0.07506942109910.534611970885-0.3393300816490.4653892340420.6561990221250.1974921051820.0965372640221-0.481724840049-0.4425179979310.480948301185-0.3963650301420.492617722104-0.279745212118-0.3171471530680.6803237519660.3719609393250.863191035016-14.5832508293-5.5253414259724.9801661805
100.1371344079520.0257051873054-0.01303597057480.04492450208140.02767587957570.205021420223-0.356575516093-0.23606620181-0.4393445630970.774052018650.11419949482-0.00664808087820.613795602250.517059559672-0.01257058361230.776708584150.00501349155203-0.2103727494830.7922405129630.2523363730221.02916614252-9.29088827213-23.36586860933.6178597848
110.0171591831173-0.02271541402160.03832973170290.0305079979853-0.05067002200420.08066481135540.0208749538714-0.0321849460844-0.302648276920.460421438051-0.06511303652390.2131527612440.516658946496-0.393355491363-7.50040254066E-51.05372015963-0.368387531544-0.2523116422681.276333254530.490117321151.61520815314-7.63010420193-23.550303698530.0544332765
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 7 through 52 )AA7 - 521 - 46
22chain 'A' and (resid 53 through 154 )AA53 - 15447 - 148
33chain 'A' and (resid 155 through 355 )AA155 - 355149 - 349
44chain 'A' and (resid 356 through 668 )AA356 - 668350 - 644
55chain 'B' and (resid 1 through 15 )BB1 - 15
66chain 'C' and (resid 3 through 13 )CC3 - 13
77chain 'D' and (resid 4 through 245 )DD4 - 2451 - 242
88chain 'D' and (resid 246 through 342 )DD246 - 342243 - 337
99chain 'D' and (resid 343 through 666 )DD343 - 666338 - 646
1010chain 'E' and (resid 1 through 13 )EE1 - 13
1111chain 'F' and (resid 5 through 13 )FF5 - 13

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