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- PDB-9njh: Translocated product complex of DNA polymerase iota with DNA (tem... -

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Basic information

Entry
Database: PDB / ID: 9njh
TitleTranslocated product complex of DNA polymerase iota with DNA (template A)
Components
  • DNA (5'-D(P*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-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
DNA / DNA (> 10) / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsFrevert, Z. / 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
DepositionFeb 27, 2025Deposition 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*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2563
Polymers52,2162
Non-polymers401
Water1,36976
1
A: DNA polymerase iota
B: DNA (5'-D(P*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules

A: DNA polymerase iota
B: DNA (5'-D(P*AP*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,5126
Polymers104,4314
Non-polymers802
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area7660 Å2
ΔGint-89 kcal/mol
Surface area37840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.926, 97.926, 194.974
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
Components on special symmetry positions
IDModelComponents
11A-668-

HOH

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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*GP*GP*GP*TP*CP*CP*TP*AP*GP*GP*AP*CP*CP*C)-3')


Mass: 5188.360 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: self-annealing DNA / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.47 Å3/Da / Density % sol: 50.29 %
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: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Feb 8, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.29→48.96 Å / Num. obs: 25733 / % possible obs: 100 % / Redundancy: 38.7 % / CC1/2: 1 / Rpim(I) all: 0.024 / Net I/σ(I): 26.9
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 39.2 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2462 / CC1/2: 0.38 / Rpim(I) all: 0.399 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.29→48.96 Å / SU ML: 0.3662 / Cross valid method: FREE R-VALUE / Phase error: 32.5203
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2884 1286 5.01 %
Rwork0.2641 24368 -
obs0.2653 25733 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.95 Å2
Refinement stepCycle: LAST / Resolution: 2.29→48.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 308 1 76 3278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01193301
X-RAY DIFFRACTIONf_angle_d1.6364517
X-RAY DIFFRACTIONf_chiral_restr0.1252527
X-RAY DIFFRACTIONf_plane_restr0.0166523
X-RAY DIFFRACTIONf_dihedral_angle_d21.00551293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.380.4081410.37772641X-RAY DIFFRACTION100
2.38-2.490.35981440.34422636X-RAY DIFFRACTION100
2.49-2.620.36421380.32242646X-RAY DIFFRACTION99.96
2.62-2.790.31221290.30652676X-RAY DIFFRACTION100
2.79-30.34081500.31112667X-RAY DIFFRACTION100
3-3.30.35641480.28722682X-RAY DIFFRACTION100
3.3-3.780.26651510.25612708X-RAY DIFFRACTION100
3.78-4.760.26761310.22772764X-RAY DIFFRACTION99.83
4.76-48.960.25161540.2452948X-RAY DIFFRACTION99.87

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