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- PDB-9y1i: S180R human DNA polymerase beta, Ternary complex dG:dCmpCpp -

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Basic information

Entry
Database: PDB / ID: 9y1i
TitleS180R human DNA polymerase beta, Ternary complex dG:dCmpCpp
Components
  • DNA polymerase beta
  • Downstream
  • Primer strand
  • Template strand
KeywordsREPLICATION / polymerase
Function / homology
Function and homology information


Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / pyrimidine dimer repair / POLB-Dependent Long Patch Base Excision Repair / homeostasis of number of cells / PCNA-Dependent Long Patch Base Excision Repair ...Resolution of AP sites via the single-nucleotide replacement pathway / immunoglobulin heavy chain V-D-J recombination / Resolution of AP sites via the multiple-nucleotide patch replacement pathway / Abasic sugar-phosphate removal via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / pyrimidine dimer repair / POLB-Dependent Long Patch Base Excision Repair / homeostasis of number of cells / PCNA-Dependent Long Patch Base Excision Repair / 5'-deoxyribose-5-phosphate lyase activity / response to hyperoxia / lymph node development / salivary gland morphogenesis / somatic hypermutation of immunoglobulin genes / spleen development / base-excision repair, gap-filling / DNA-(apurinic or apyrimidinic site) endonuclease activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / response to gamma radiation / spindle microtubule / base-excision repair / double-strand break repair via nonhomologous end joining / DNA-templated DNA replication / intrinsic apoptotic signaling pathway in response to DNA damage / neuron apoptotic process / response to ethanol / microtubule binding / in utero embryonic development / DNA-directed DNA polymerase / microtubule / damaged DNA binding / DNA-directed DNA polymerase activity / Ub-specific processing proteases / lyase activity / inflammatory response / DNA repair / DNA damage response / enzyme binding / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytoplasm
Similarity search - Function
DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase X family / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase family X, binding site ...DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase X family / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
Chem-XC5 / DNA / DNA (> 10) / DNA polymerase beta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsEckenroth, B.E. / Doublie, S.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA281044 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R50-CA233185 United States
CitationJournal: Biochemistry / Year: 2026
Title: The S180R Human Germline Variant of DNA Polymerase beta Is a Low Fidelity Enzyme with Reduced Flexibility of the Fingers Domain.
Authors: Sawyer, D.L. / Eckenroth, B.E. / Chavira, C. / Alnajjar, K. / Hanley, J.P. / Dragon, J.A. / Doublie, S. / Sweasy, J.B.
History
DepositionAug 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 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 beta
T: Template strand
P: Primer strand
D: Downstream
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,37310
Polymers47,7784
Non-polymers5956
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5230 Å2
ΔGint-83 kcal/mol
Surface area19920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.776, 79.887, 55.359
Angle α, β, γ (deg.)90.00, 107.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase beta / 5'-deoxyribose-phosphate lyase / 5'-dRP lyase / AP lyase


Mass: 38311.785 Da / Num. of mol.: 1 / Mutation: S180R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLB / Production host: Escherichia coli (E. coli)
References: UniProt: P06746, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases, DNA-(apurinic or apyrimidinic site) lyase

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DNA chain , 3 types, 3 molecules TPD

#2: DNA chain Template strand


Mass: 4869.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Primer strand


Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain Downstream


Mass: 1536.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 390 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-XC5 / 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine


Mass: 465.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N3O12P3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Description: Cryoprotection with 19% PEG 3350, 150 mM sodium acetate, 50 mM magnesium chloride, 50 mM magnesium acetate, 50 mM HEPES, 1 mM TECP, 15% ethylene glycol with 1 mM dNTP
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 13-16% PEG 3350, 150-300 mM sodium acetate, 50 mM HEPES, 1 mM TECP 250uM protein with 300 uM DNA assembly mixed 1:1 with reagent

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.54 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Nov 20, 2023
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→24 Å / Num. obs: 43866 / % possible obs: 98.89 % / Redundancy: 3.86 % / Biso Wilson estimate: 21.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.034 / Rrim(I) all: 0.068 / Net I/σ(I): 17.8
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 2.72 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 2052 / CC1/2: 0.871 / Rpim(I) all: 0.202 / Rrim(I) all: 0.363 / % possible all: 89.41

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PROTEUM PLUS3data scaling
PROTEUM PLUS3data reduction
PDB_EXTRACTdata extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→23.78 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.38 / Stereochemistry target values: ML
Details: Model refinement uses I+/I-. Data collection statistics reported for I-mean so % completeness and number or reflections may differ between tables.
RfactorNum. reflection% reflection
Rfree0.2126 4362 9.94 %
Rwork0.1559 --
obs0.1616 43866 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→23.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2613 632 33 384 3662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043431
X-RAY DIFFRACTIONf_angle_d0.6694762
X-RAY DIFFRACTIONf_dihedral_angle_d19.5491358
X-RAY DIFFRACTIONf_chiral_restr0.042519
X-RAY DIFFRACTIONf_plane_restr0.006505
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.170.28911050.2297956X-RAY DIFFRACTION70
2.17-2.20.28341210.23211057X-RAY DIFFRACTION76
2.2-2.230.27321330.22061150X-RAY DIFFRACTION88
2.23-2.250.27461560.19941278X-RAY DIFFRACTION95
2.26-2.280.27881450.1971322X-RAY DIFFRACTION100
2.28-2.320.25531500.20041407X-RAY DIFFRACTION100
2.32-2.350.27071660.18221300X-RAY DIFFRACTION100
2.35-2.380.23061490.20531346X-RAY DIFFRACTION100
2.38-2.420.26961590.19791395X-RAY DIFFRACTION99
2.42-2.460.2681490.191239X-RAY DIFFRACTION99
2.46-2.50.27081550.18571371X-RAY DIFFRACTION98
2.5-2.550.23621420.18381337X-RAY DIFFRACTION98
2.55-2.60.24631590.17421342X-RAY DIFFRACTION100
2.6-2.650.30131330.1811373X-RAY DIFFRACTION100
2.65-2.710.27941500.1821353X-RAY DIFFRACTION100
2.71-2.770.21151270.18511375X-RAY DIFFRACTION100
2.77-2.840.2561550.16451336X-RAY DIFFRACTION100
2.84-2.920.25011770.17341327X-RAY DIFFRACTION100
2.92-30.17641310.16771364X-RAY DIFFRACTION100
3-3.10.23841740.16891333X-RAY DIFFRACTION100
3.1-3.210.22721470.15631336X-RAY DIFFRACTION100
3.21-3.340.15091230.14471396X-RAY DIFFRACTION100
3.34-3.490.22381590.13811372X-RAY DIFFRACTION100
3.49-3.670.17841180.12751359X-RAY DIFFRACTION99
3.67-3.90.17141450.12771379X-RAY DIFFRACTION100
3.9-4.20.15741310.12231341X-RAY DIFFRACTION100
4.2-4.620.15441650.11331350X-RAY DIFFRACTION100
4.62-5.280.17831390.13261324X-RAY DIFFRACTION100
5.28-6.630.19571380.12891386X-RAY DIFFRACTION100
6.65-23.780.13791610.12091300X-RAY DIFFRACTION97
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)
10.1006-0.02360.0210.02410.13720.21110.44540.48010.7567-0.8181-0.1771-0.4957-0.10830.24190.00940.50540.06140.19420.52940.10520.384825.25224.4356-2.7136
20.4885-0.41620.2870.4109-0.01390.62420.0842-0.02320.351-0.1874-0.1184-0.4599-0.06180.1548-0.02150.2036-0.03550.03750.1472-0.00050.212912.55916.343614.4084
31.3961-0.1444-0.20622.54290.4761.23560.06420.04910.0011-0.23410.0317-0.19190.09720.28910.00010.19750.04930.00530.2083-0.01340.155622.2984-8.561510.149
41.43750.2434-0.62481.0681-0.33671.6260.0997-0.2485-0.08790.136-0.0438-0.2233-0.11290.3352-0.00340.1293-0.0082-0.04010.22-0.02130.18517.3317.340330.33
51.31590.31630.14441.7721-0.1242.57760.0112-0.07540.0115-0.02150.02630.2083-0.1126-0.39530.00490.08020.02690.01390.19130.00590.1704-6.305210.715720.1657
61.2918-0.3228-0.31221.82380.38941.8962-0.03710.2350.0286-0.62580.0369-0.1115-0.0551-0.005-0.00040.2929-0.0177-0.0080.1919-0.0130.17643.07698.6408-1.8606
70.5462-0.36960.60242.575-1.63052.16540.0175-0.23630.3401-0.5684-0.5778-0.70180.2127-0.2232-0.40310.3182-0.06870.02350.2134-0.05170.572718.818930.857417.8802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((chain D and resid 1:5) or (chain T and resid 1:6))
2X-RAY DIFFRACTION2((chain P and resid 6:10) or (chain T and resid 7:11))
3X-RAY DIFFRACTION3chain A and resid 12:90
4X-RAY DIFFRACTION4chain A and resid 91:150
5X-RAY DIFFRACTION5chain A and resid 151:260
6X-RAY DIFFRACTION6chain A and resid 261:335
7X-RAY DIFFRACTION7((chain P and resid 1:5) or (chain T and resid 12:16))

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