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- PDB-9d6n: Loop-Deleted DNA Polymerase Theta in Complex with a dsDNA Overhan... -

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Basic information

Entry
Database: PDB / ID: 9d6n
TitleLoop-Deleted DNA Polymerase Theta in Complex with a dsDNA Overhang and an Allostertic Inhibitor
Components
  • DNA Primer
  • DNA Template
  • DNA polymerase theta
KeywordsDNA BINDING PROTEIN / DNA Polymerase Theta / DNA Polymerase / Allosteric Inhibitor / Protein-DNA 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 / replication fork processing / mitochondrial nucleoid / site of DNA damage / 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 / replication fork processing / mitochondrial nucleoid / site of DNA damage / 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 / 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 / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA repair / DNA damage response / chromatin binding / 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: 2.43 Å
AuthorsFried, W. / Chen, X.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM130889 United States
CitationJournal: To Be Published
Title: Loop-Deleted DNA Polymerase Theta in Complex with a dsDNA Overhang and an Allostertic Inhibitor
Authors: Fried, W. / Chen, X.S.
History
DepositionAug 15, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: 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
E: DNA Template
F: DNA Primer
B: DNA polymerase theta
C: DNA Template
D: DNA Primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,62312
Polymers168,4596
Non-polymers2,1646
Water5,549308
1
A: DNA polymerase theta
E: DNA Template
F: DNA Primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3116
Polymers84,2293
Non-polymers1,0823
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-23 kcal/mol
Surface area32350 Å2
MethodPISA
2
B: DNA polymerase theta
C: DNA Template
D: DNA Primer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3116
Polymers84,2293
Non-polymers1,0823
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-22 kcal/mol
Surface area32270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.119, 171.119, 118.026
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein DNA polymerase theta / DNA polymerase eta


Mass: 72589.812 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 helicase, DNA-directed DNA polymerase, RNA-directed DNA polymerase

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DNA chain , 2 types, 4 molecules ECFD

#2: DNA chain DNA Template


Mass: 7372.730 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA Primer


Mass: 4266.768 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 314 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-A1A2C / 2-{3-[(2R)-3-(dimethylamino)-2-hydroxypropyl]-2-oxoimidazolidin-1-yl}-4,6-bis(trifluoromethyl)phenyl (4-fluorophenyl)(methyl)carbamate


Mass: 566.469 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25F7N4O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Bis Tris Propane pH 7.5, 16% PEG 3350, 0.23M Sodium Citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 10, 2024
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.43→92.39 Å / Num. obs: 75169 / % possible obs: 100 % / Redundancy: 20.3 % / Biso Wilson estimate: 55.21 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.054 / Rrim(I) all: 0.247 / Net I/σ(I): 12
Reflection shellResolution: 2.43→2.52 Å / Redundancy: 20.6 % / Rmerge(I) obs: 3.956 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 7435 / CC1/2: 0.376 / Rpim(I) all: 0.883 / Rrim(I) all: 4.054 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHASERphasing
Coot0.9.8.92model building
DIALS3.8data reduction
DIALS3.8data scaling
BOSdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.43→92.32 Å / SU ML: 0.3644 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.8805
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2374 3794 5.05 %
Rwork0.21 71360 -
obs0.2114 75154 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.97 Å2
Refinement stepCycle: LAST / Resolution: 2.43→92.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10004 1554 140 308 12006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002712079
X-RAY DIFFRACTIONf_angle_d0.52216644
X-RAY DIFFRACTIONf_chiral_restr0.0381839
X-RAY DIFFRACTIONf_plane_restr0.00471857
X-RAY DIFFRACTIONf_dihedral_angle_d19.20154578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.460.34191540.31762587X-RAY DIFFRACTION99.71
2.46-2.490.331390.30622623X-RAY DIFFRACTION99.96
2.49-2.530.2861180.28472619X-RAY DIFFRACTION99.96
2.53-2.560.33291400.28572643X-RAY DIFFRACTION99.96
2.56-2.60.32321460.28452626X-RAY DIFFRACTION100
2.6-2.640.31621470.2872597X-RAY DIFFRACTION99.96
2.64-2.690.31421470.29662631X-RAY DIFFRACTION100
2.69-2.730.36881060.33292630X-RAY DIFFRACTION100
2.73-2.780.33991580.30712589X-RAY DIFFRACTION99.96
2.78-2.830.35131540.29472625X-RAY DIFFRACTION100
2.83-2.890.2761450.28812647X-RAY DIFFRACTION99.96
2.89-2.960.32961110.26132634X-RAY DIFFRACTION100
2.96-3.020.31161210.25742650X-RAY DIFFRACTION99.96
3.02-3.10.27961510.25682654X-RAY DIFFRACTION99.96
3.1-3.180.3011190.24942619X-RAY DIFFRACTION100
3.18-3.280.28231260.2472634X-RAY DIFFRACTION99.96
3.28-3.380.30621200.26242656X-RAY DIFFRACTION100
3.38-3.50.29351410.22452644X-RAY DIFFRACTION100
3.5-3.640.22651610.19642632X-RAY DIFFRACTION100
3.64-3.810.21331200.18552679X-RAY DIFFRACTION100
3.81-4.010.21141510.17962617X-RAY DIFFRACTION100
4.01-4.260.22991670.17422639X-RAY DIFFRACTION100
4.26-4.590.1781460.15772641X-RAY DIFFRACTION100
4.59-5.050.18391840.16142640X-RAY DIFFRACTION100
5.05-5.780.18011220.18212704X-RAY DIFFRACTION100
5.78-7.290.21671490.19562697X-RAY DIFFRACTION100
7.29-92.320.18221510.1592803X-RAY DIFFRACTION99.8
Refinement TLS params.Method: refined / Origin x: 4.14725985255 Å / Origin y: -60.3650517121 Å / Origin z: 45.957447345 Å
111213212223313233
T0.36604592112 Å2-0.0531134872952 Å20.0784080434519 Å2-0.356858134653 Å2-0.00180787655335 Å2--0.460255546512 Å2
L0.20232446965 °20.0997218160666 °20.0815498667111 °2-0.34638775698 °20.0868493820412 °2--0.873783495412 °2
S0.0765101763096 Å °-0.0608929201888 Å °0.0514350858112 Å °0.00514082211715 Å °0.00720466026786 Å °0.00241139256819 Å °0.190544969881 Å °-0.0882240808088 Å °-0.0853091923247 Å °
Refinement TLS groupSelection details: all

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