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- PDB-9dqu: Product complex of DNA polymerase iota with Pyrophosphate -

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Basic information

Entry
Database: PDB / ID: 9dqu
TitleProduct complex of DNA polymerase iota with Pyrophosphate
Components
  • DNA (5'-D(P*AP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*CP*T)-3')
  • DNA polymerase iota
KeywordsREPLICATION / DNA / Polymerase / Lesion
Function / homology
Function and homology information


error-prone translesion synthesis / translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / nuclear speck ...error-prone translesion synthesis / translesion synthesis / Translesion synthesis by POLI / Termination of translesion DNA synthesis / cytoplasmic ribonucleoprotein granule / DNA-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / nuclear speck / DNA repair / nucleoplasm / metal ion binding
Similarity search - Function
HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. ...HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
PYROPHOSPHATE 2- / DNA / DNA (> 10) / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFrevert, Z. / Reusch, D. / Freudenthal, B. / Washington, M.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM081433 United States
CitationJournal: Nat Commun / Year: 2025
Title: Visualizing DNA polymerase iota catalyze Hoogsteen-directed DNA synthesis.
Authors: Frevert, Z. / Reusch, D.T. / Gildenberg, M.S. / Jordan, S.M. / Ryan, B.J. / Freudenthal, B.D. / Washington, M.T.
History
DepositionSep 24, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase iota
B: DNA (5'-D(P*AP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0826
Polymers52,8332
Non-polymers2494
Water2,036113
1
A: DNA polymerase iota
B: DNA (5'-D(P*AP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*CP*T)-3')
hetero molecules

A: DNA polymerase iota
B: DNA (5'-D(P*AP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,16412
Polymers105,6664
Non-polymers4988
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area10560 Å2
ΔGint-126 kcal/mol
Surface area36850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.488, 97.488, 201.550
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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Components

#1: Protein DNA polymerase iota / Eta2 / RAD30 homolog B


Mass: 47027.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLI, RAD30B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UNA4, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(P*AP*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*CP*T)-3')


Mass: 5805.761 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
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: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 100 mM HEPES pH 7 1.5 -1.8 M Ammonium Sulfate 5 mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Mar 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→43.88 Å / Num. obs: 29552 / % possible obs: 100 % / Redundancy: 20.6 % / Biso Wilson estimate: 36.82 Å2 / CC1/2: 1 / Rpim(I) all: 0.026 / Net I/σ(I): 22.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 20.6 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2894 / CC1/2: 0.788 / Rpim(I) all: 0.505 / % possible all: 100

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Processing

Software
NameVersionClassification
Cootmodel building
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→43.27 Å / SU ML: 0.3221 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3235
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2775 1467 4.96 %
Rwork0.2367 28085 -
obs0.2387 29552 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→43.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 349 12 113 3367
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043331
X-RAY DIFFRACTIONf_angle_d0.70824564
X-RAY DIFFRACTIONf_chiral_restr0.0422531
X-RAY DIFFRACTIONf_plane_restr0.0073524
X-RAY DIFFRACTIONf_dihedral_angle_d15.5443561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.32781460.33122748X-RAY DIFFRACTION99.93
2.28-2.370.35591420.29362748X-RAY DIFFRACTION99.93
2.37-2.480.33661610.2692723X-RAY DIFFRACTION99.86
2.48-2.610.29361360.26792755X-RAY DIFFRACTION99.97
2.61-2.770.35521500.27172779X-RAY DIFFRACTION99.97
2.77-2.990.38751280.29182783X-RAY DIFFRACTION99.93
2.99-3.290.28761510.25032793X-RAY DIFFRACTION100
3.29-3.760.26661390.22752846X-RAY DIFFRACTION99.9
3.76-4.740.22651520.18842856X-RAY DIFFRACTION100
4.74-43.270.23811620.21483054X-RAY DIFFRACTION99.78

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