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- PDB-9ddr: Ternary substrate complex of DNA polymerase iota with DNA (templa... -

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Basic information

Entry
Database: PDB / ID: 9ddr
TitleTernary substrate complex of DNA polymerase iota with DNA (template A), Ca2+, and dTTP
Components
  • DNA (5'-D(P*AP*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
THYMIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionAug 28, 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*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0915
Polymers52,5292
Non-polymers5623
Water2,594144
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*C)-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*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,18210
Polymers105,0584
Non-polymers1,1256
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area10650 Å2
ΔGint-110 kcal/mol
Surface area36750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.556, 97.556, 202.148
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: Polymerase Iota catalytic core / 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*C)-3')


Mass: 5501.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: self-annealing DNA / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE


Mass: 482.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N2O14P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
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: May 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→47.42 Å / Num. obs: 31750 / % possible obs: 99.89 % / Redundancy: 2 % / Biso Wilson estimate: 42.04 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01534 / Rpim(I) all: 0.01534 / Rrim(I) all: 0.02169 / Net I/σ(I): 31.1
Reflection shellResolution: 2.15→2.227 Å / Rmerge(I) obs: 0.2874 / Num. unique obs: 3105 / CC1/2: 0.894 / CC star: 0.972 / % possible all: 99.94

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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: 2.15→47.42 Å / SU ML: 0.307 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.5222
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2802 1595 5.03 %
Rwork0.2368 30127 -
obs0.2389 31722 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.28 Å2
Refinement stepCycle: LAST / Resolution: 2.15→47.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2893 329 31 144 3397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00463331
X-RAY DIFFRACTIONf_angle_d0.79754564
X-RAY DIFFRACTIONf_chiral_restr0.0422530
X-RAY DIFFRACTIONf_plane_restr0.0079524
X-RAY DIFFRACTIONf_dihedral_angle_d20.19971306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.220.33651560.30262668X-RAY DIFFRACTION99.96
2.22-2.30.35231650.31442630X-RAY DIFFRACTION99.89
2.3-2.390.40581340.29592697X-RAY DIFFRACTION99.86
2.39-2.50.33581240.292704X-RAY DIFFRACTION99.82
2.5-2.630.31641400.282707X-RAY DIFFRACTION100
2.63-2.80.3071540.27462676X-RAY DIFFRACTION99.72
2.8-3.010.30841330.28772732X-RAY DIFFRACTION99.97
3.01-3.310.27991520.25092735X-RAY DIFFRACTION100
3.32-3.790.28691580.22692748X-RAY DIFFRACTION99.9
3.8-4.780.22831440.18682810X-RAY DIFFRACTION99.97
4.78-47.420.2521350.21443020X-RAY DIFFRACTION99.87

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