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- PDB-9dr7: Product complex of DNA polymerase iota with 2 monophosphates -

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Basic information

Entry
Database: PDB / ID: 9dr7
TitleProduct complex of DNA polymerase iota with 2 monophosphates
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
PHOSPHATE ION / DNA / DNA (> 10) / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 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
Citation
Journal: 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.
#1: Journal: Bull Soc Ophtalmol Fr / Year: 1987
Title: [Treatment of vitreous hemorrhages. Rare causes].
Authors: Aracil, P.
History
DepositionSep 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 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 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)53,0967
Polymers52,8332
Non-polymers2635
Water1,49583
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)106,19214
Polymers105,6664
Non-polymers52610
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area10940 Å2
ΔGint-164 kcal/mol
Surface area37340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.190, 98.190, 202.340
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
Details: catalytic core of DNA polymerase Iota / 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 / Details: self-annealing DNA / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / 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.: 83 / 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: 2.66 Å3/Da / Density % sol: 53.84 %
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: 2.45→49.1 Å / Num. obs: 21926 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 43.03 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.049 / Net I/σ(I): 13.2
Reflection shellResolution: 2.45→2.56 Å / Redundancy: 20 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2657 / CC1/2: 0.811 / Rpim(I) all: 0.469 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→49.09 Å / SU ML: 0.3443 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.2932
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3119 1109 5.06 %
Rwork0.2537 20817 -
obs0.2566 21926 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.96 Å2
Refinement stepCycle: LAST / Resolution: 2.45→49.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 349 13 83 3338
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00323331
X-RAY DIFFRACTIONf_angle_d0.60864563
X-RAY DIFFRACTIONf_chiral_restr0.0393531
X-RAY DIFFRACTIONf_plane_restr0.0057524
X-RAY DIFFRACTIONf_dihedral_angle_d15.1341559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.560.39741250.3182532X-RAY DIFFRACTION99.89
2.56-2.70.33291390.28692546X-RAY DIFFRACTION99.93
2.7-2.870.34431340.30752548X-RAY DIFFRACTION99.89
2.87-3.090.39741330.31212577X-RAY DIFFRACTION99.82
3.09-3.40.34211390.26622585X-RAY DIFFRACTION99.89
3.4-3.890.30731360.25622596X-RAY DIFFRACTION99.74
3.89-4.90.26681400.21232636X-RAY DIFFRACTION99.39
4.9-49.090.28021630.22992797X-RAY DIFFRACTION99.4

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