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- PDB-8e24: Human DNA polymerase theta in complex with allosteric inhibitor -

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Basic information

Entry
Database: PDB / ID: 8.0E+24
TitleHuman DNA polymerase theta in complex with allosteric inhibitor
Components
  • (DNA) x 2
  • DNA polymerase thetaPOLQ
KeywordsDNA BINDING PROTEIN/DNA / DNA polymerase theta / inhibitor / allosteric / complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA 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 / Chem-UA6 / DNA / DNA (> 10) / DNA polymerase theta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsMader, P. / Pau, V.P.T. / Sicheri, F.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN 143277 Canada
Other private
Citation
Journal: J.Med.Chem. / Year: 2022
Title: Identification of RP-6685 , an Orally Bioavailable Compound that Inhibits the DNA Polymerase Activity of Pol theta.
Authors: Bubenik, M. / Mader, P. / Mochirian, P. / Vallee, F. / Clark, J. / Truchon, J.F. / Perryman, A.L. / Pau, V. / Kurinov, I. / Zahn, K.E. / Leclaire, M.E. / Papp, R. / Mathieu, M.C. / Hamel, M. ...Authors: Bubenik, M. / Mader, P. / Mochirian, P. / Vallee, F. / Clark, J. / Truchon, J.F. / Perryman, A.L. / Pau, V. / Kurinov, I. / Zahn, K.E. / Leclaire, M.E. / Papp, R. / Mathieu, M.C. / Hamel, M. / Duffy, N.M. / Godbout, C. / Casas-Selves, M. / Falgueyret, J.P. / Baruah, P.S. / Nicolas, O. / Stocco, R. / Poirier, H. / Martino, G. / Fortin, A.B. / Roulston, A. / Chefson, A. / Dorich, S. / St-Onge, M. / Patel, P. / Pellerin, C. / Ciblat, S. / Pinter, T. / Barabe, F. / El Bakkouri, M. / Parikh, P. / Gervais, C. / Sfeir, A. / Mamane, Y. / Morris, S.J. / Black, W.C. / Sicheri, F. / Gallant, M.
#1: Journal: J. Med. Chem. / Year: 2022
Title: Identification of Lead RP-6685: an orally bioavailable compound that inhibits the DNA polymerase activity of Pol Theta
Authors: Bubenik, M. / Mader, P. / Mochirian, P. / Vallee, F. / Clark, J. / Truchon, J.F. / Perryman, A.L. / Pau, V. / Kurinov, I. / Zahn, K.E. / Leclaire, M.E. / Papp, R. / Mathieu, M.C. / Hamel, M. ...Authors: Bubenik, M. / Mader, P. / Mochirian, P. / Vallee, F. / Clark, J. / Truchon, J.F. / Perryman, A.L. / Pau, V. / Kurinov, I. / Zahn, K.E. / Leclaire, M.E. / Papp, R. / Mathieu, M.C. / Hamel, M. / Duffy, N.M. / Godbout, C. / Casas-Selves, M. / Falgueyret, J.P. / Baruah, P.S. / Nicolas, O. / Stocco, R. / Poirier, H. / Martino, J. / Fortin, A.B. / Chefson, A. / Dorich, S. / St-Onge, M. / Patel, P. / Pellerin, C. / Ciblat, S. / Pinter, T. / Barabe, F. / El Bakkouri, M. / Parikh, P. / Gervais, C. / Mamane, Y. / Morris, S.J. / Black, C.W. / Sicheri, F. / Gallant, M.
History
DepositionAug 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
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
B: DNA
C: DNA
D: DNA polymerase theta
E: DNA
F: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,67012
Polymers168,7126
Non-polymers1,9586
Water2,774154
1
A: DNA polymerase theta
B: DNA
C: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3356
Polymers84,3563
Non-polymers9793
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-20 kcal/mol
Surface area30300 Å2
MethodPISA
2
D: DNA polymerase theta
E: DNA
F: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3356
Polymers84,3563
Non-polymers9793
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-21 kcal/mol
Surface area29600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)263.739, 66.287, 156.662
Angle α, β, γ (deg.)90.000, 126.140, 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 / POLQ / DNA polymerase eta


Mass: 75200.070 Da / Num. of mol.: 2
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

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DNA chain , 2 types, 4 molecules BECF

#2: DNA chain DNA /


Mass: 5157.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA /


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

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Non-polymers , 4 types, 160 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-UA6 / 2-[2,4-bis(trifluoromethyl)phenyl]-N-phenyl-N-[3-(pyridazin-3-yl)prop-2-yn-1-yl]acetamide


Mass: 463.375 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H15F6N3O / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 62.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 16% PEG 3350, 0.2M diammonium tartrate, 2% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.34→126.52 Å / Num. obs: 74032 / % possible obs: 79.9 % / Redundancy: 2.7 % / Biso Wilson estimate: 57.54 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.101 / Net I/σ(I): 8.92
Reflection shellResolution: 2.34→2.49 Å / Redundancy: 2.07 % / Mean I/σ(I) obs: 2.16 / Num. unique obs: 9002 / CC1/2: 0.422 / % possible all: 60.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X0Q

4x0q


Resolution: 2.34→126.52 Å / SU ML: 0.602 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 41.3196
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2662 3685 4.99 %
Rwork0.2314 70139 -
obs0.2332 73824 79.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.29 Å2
Refinement stepCycle: LAST / Resolution: 2.34→126.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9888 931 128 154 11101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001911254
X-RAY DIFFRACTIONf_angle_d0.463815452
X-RAY DIFFRACTIONf_chiral_restr0.03661740
X-RAY DIFFRACTIONf_plane_restr0.00361821
X-RAY DIFFRACTIONf_dihedral_angle_d14.39834126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.34-2.380.6193570.54331478X-RAY DIFFRACTION43.65
2.38-2.410.5471890.5591881X-RAY DIFFRACTION56.09
2.41-2.440.57341190.54492285X-RAY DIFFRACTION67.68
2.44-2.480.5381360.5082304X-RAY DIFFRACTION69.61
2.48-2.520.55831220.50252355X-RAY DIFFRACTION70.61
2.52-2.560.49381220.49472482X-RAY DIFFRACTION73.35
2.56-2.60.4941280.48162433X-RAY DIFFRACTION73.85
2.6-2.650.49621160.49142544X-RAY DIFFRACTION74.12
2.65-2.70.47451310.47212518X-RAY DIFFRACTION75.86
2.7-2.760.62671450.5332564X-RAY DIFFRACTION76.05
2.76-2.820.54131420.47682389X-RAY DIFFRACTION72.56
2.82-2.880.4991460.40812691X-RAY DIFFRACTION79.49
2.88-2.950.43211380.36872743X-RAY DIFFRACTION82.01
2.95-3.030.42041380.3342810X-RAY DIFFRACTION82.83
3.03-3.120.34341430.31232811X-RAY DIFFRACTION84.16
3.12-3.220.3041620.28142886X-RAY DIFFRACTION86.44
3.22-3.340.27721580.26883014X-RAY DIFFRACTION88.58
3.34-3.470.31511550.26662771X-RAY DIFFRACTION82.26
3.47-3.630.24411600.20713033X-RAY DIFFRACTION91.44
3.63-3.820.23621700.18673150X-RAY DIFFRACTION92.92
3.82-4.060.20631660.17343174X-RAY DIFFRACTION93.82
4.06-4.380.21261860.15773124X-RAY DIFFRACTION92.17
4.38-4.820.16821510.13853053X-RAY DIFFRACTION90.15
4.82-5.510.19991830.15413231X-RAY DIFFRACTION94.41
5.51-6.940.20441450.19223102X-RAY DIFFRACTION90.37
6.95-126.520.20221770.17843313X-RAY DIFFRACTION93.22
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)
11.87311876382-0.6215246111310.04508224958710.6585986517330.02167449229550.356256519948-0.115357123620.583057278279-0.0508033375497-0.3098878709670.130703664605-0.3501078226860.1228778637350.678426540613-6.7552326581E-50.4269029054330.01115393430290.03783200975640.792692368376-0.05342259393370.46557005201462.1804033461-8.6087660024115.6315642843
21.24002732134-0.481327791024-0.4095568057430.6280252709140.6874617011751.77780326011-0.1220984738610.114338803373-0.1282183876680.1484798336110.0004452026095170.003661629978250.04485024541590.381670596032-3.34843655265E-50.3809406875530.01208659184870.009625510618270.48886112888-0.02414664978440.41961860883755.3276518898-7.7789153989330.5088399637
32.24891195532-1.421818988910.2763711169293.18720073147-0.5286404984950.608723228284-0.1915426400740.1310414338810.4445692484960.331392984840.162263084856-0.117973250963-0.257378553485-0.116431944841-0.06779531039950.5479717454470.0158419098040.02302706543880.1731466658940.0534689860460.42658067989433.284066900622.843497969943.2625391428
42.11546406878-0.733032740011-0.6412596319941.614680879140.2255829671232.09223556316-0.232243990571-0.163302671985-0.2273600270970.4185411345120.138144402930.2958716264390.225583946729-0.229806504086-0.007025824076940.433733613014-0.04651238440160.07789296677540.179268715502-0.003545980288120.4083037802432.0260196026-2.6171661462348.9121821529
52.03673427736-1.03952426929-0.2814403869761.584874691820.02021119419040.0943126023339-0.790561360383-1.087098761450.850339613780.5167877570740.702762154051-0.490719653559-1.752732712920.657990570841-0.2039449394270.967820828012-0.444764816925-0.290188716550.514808046973-0.1973421597620.69929574035747.976657563914.177197722653.4791743355
61.014941971720.48155760225-1.424332363691.4339308394-0.6683424128272.17079822028-0.676037775071-1.79452355075-0.0784160630129-0.5174911105010.560226444388-2.58858094311-0.221415188761.94313287946-0.5407060911690.404715334856-0.149363693148-0.1941533090851.00252777196-0.1606527393791.6398864144847.576163770716.018239816449.7801852628
71.258610753180.1648802683580.5511689162271.70094798366-0.6490977236311.608688645670.07694162128690.00997410970844-0.155755442309-0.192836455980.1941441636160.1537503123050.222138770856-0.2803229742240.0001880154542540.3567882934520.0508704404917-0.01395449516720.7288516959740.07261819687930.514051491599-48.742598198-24.14417041435.77098694619
82.475364956660.6443745900021.210693257041.53124234785-0.3936198751571.49072540427-0.0504613753091-0.258239658306-0.3027700852880.285016678698-0.00690812880083-0.125760488915-0.0565768258877-0.0346503384898-0.0006061564782650.3668803704850.06505385212430.02940922874660.6797743894580.1523308418680.43737341337-39.2944355554-20.35147811120.0095295178
91.28496844393-0.1893919768130.03400643265540.8163870857060.05713511585140.1418377732020.02042427030.215357667953-0.38548407636-0.002219818098430.0994829226922-0.204590970608-0.1623177452810.2528340540150.002945606067890.527129837415-0.0516370451416-0.05408875494750.7138511674430.1144914131140.64367135164.47182122834-21.140797721321.7285366336
102.1420077186-0.4033076710270.5702014124911.45976325744-0.4635112150881.35524088472-0.0173739943134-0.1076538451010.5442291656830.3266106602250.095280648505-0.354052021819-0.625903015643-0.00274868937181-0.0007725854563470.544480360323-0.0966740448859-0.1085692938880.59192463757-0.0304283177840.616872247235-13.1547117773-3.8857823119630.4156296893
111.970956267640.1270194744040.1503975154620.7382822593870.1183577363490.596283551498-0.1217460345170.1762502665550.5506296356560.0123504517151-0.0588191365957-0.149769778939-0.721436254397-0.16235099804-0.02779164354810.5383832699280.00624415597347-0.0304031786170.4198170773950.1136649938080.480762770949-23.7697372832-2.1636595505916.4783984819
120.305674331044-0.147317536772-0.2498185407520.184267315444-0.1780156468390.8874642761770.0314437332755-0.614186851441-0.2756904308951.04556829241-0.392057783955-0.6816415256660.4517907230350.214861329177-0.132639132150.900235573716-0.0289750192321-0.2845393680350.7274200061710.1960489307980.837675040601-13.0030402181-21.504125848133.9120751936
130.1521978610190.250620286045-0.2967715804710.668756761465-0.3174453475280.705440323294-0.0248074979981-1.44280372879-0.7570637217840.445534729861-0.3067356231810.3247196465890.0346686656147-0.266651099925-0.4294888761110.694925590934-0.2304247467040.02111993608470.9411940339850.4458302941450.969412630338-11.4382451806-21.724725783630.6523618306
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1823 through 1940 )AA1823 - 19401 - 84
22chain 'A' and (resid 1941 through 2095 )AA1941 - 209585 - 239
33chain 'A' and (resid 2096 through 2317 )AA2096 - 2317240 - 388
44chain 'A' and (resid 2318 through 2589 )AA2318 - 2589389 - 644
55chain 'B' and (resid 1 through 14 )BE1 - 14
66chain 'C' and (resid 4 through 13 )CF4 - 13
77chain 'D' and (resid 1821 through 1966 )DG1821 - 19661 - 112
88chain 'D' and (resid 1967 through 2095 )DG1967 - 2095113 - 240
99chain 'D' and (resid 2096 through 2224 )DG2096 - 2224241 - 341
1010chain 'D' and (resid 2225 through 2457 )DG2225 - 2457342 - 534
1111chain 'D' and (resid 2458 through 2589 )DG2458 - 2589535 - 648
1212chain 'E' and (resid 1 through 13 )EK1 - 13
1313chain 'F' and (resid 5 through 13 )FL5 - 13

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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