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- PDB-9drc: Ternary substrate complex of DNA polymerase iota R71A mutant with... -

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Basic information

Entry
Database: PDB / ID: 9drc
TitleTernary substrate complex of DNA polymerase iota R71A mutant with DNA (template A) 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 / 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: Acta Crystallogr D Biol Crystallogr / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
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*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0055
Polymers52,4432
Non-polymers5623
Water1,09961
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)106,01010
Polymers104,8864
Non-polymers1,1256
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area9860 Å2
ΔGint-107 kcal/mol
Surface area37070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.278, 97.278, 202.828
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: 46941.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: catalytic core of DNA polymerase Iota Arginine 71 to Alanine mutant
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 / 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.: 61 / 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: 53.43 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Aug 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.45→25 Å / Num. obs: 33634 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 36.59 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.025 / Net I/σ(I): 24.1
Reflection shellResolution: 2.45→2.48 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 665 / CC1/2: 0.64 / Rpim(I) all: 0.443 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→24.89 Å / SU ML: 0.3278 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.7885
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2941 3203 9.52 %
Rwork0.2485 30431 -
obs0.2529 33634 84.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.06 Å2
Refinement stepCycle: LAST / Resolution: 2.45→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2840 329 31 61 3261
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00443302
X-RAY DIFFRACTIONf_angle_d0.59644534
X-RAY DIFFRACTIONf_chiral_restr0.0399528
X-RAY DIFFRACTIONf_plane_restr0.0044516
X-RAY DIFFRACTIONf_dihedral_angle_d20.34566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.480.2962630.3381602X-RAY DIFFRACTION38.44
2.48-2.520.3866740.3229712X-RAY DIFFRACTION45.78
2.52-2.560.3141790.3423766X-RAY DIFFRACTION48.73
2.56-2.610.4093810.3135786X-RAY DIFFRACTION51.39
2.61-2.660.3121000.2986909X-RAY DIFFRACTION58.36
2.66-2.710.34971030.31191031X-RAY DIFFRACTION65.32
2.71-2.760.36671170.29291151X-RAY DIFFRACTION74.37
2.76-2.820.3551400.30191314X-RAY DIFFRACTION84.53
2.82-2.890.31671500.29571455X-RAY DIFFRACTION93.75
2.89-2.960.30741650.28891541X-RAY DIFFRACTION97.54
2.96-3.040.30651680.30141525X-RAY DIFFRACTION99.24
3.04-3.130.31521630.27811543X-RAY DIFFRACTION99.42
3.13-3.230.39011620.2741544X-RAY DIFFRACTION99.82
3.23-3.340.37081610.24871577X-RAY DIFFRACTION100
3.34-3.480.2841690.25431561X-RAY DIFFRACTION99.88
3.48-3.640.27231610.24841524X-RAY DIFFRACTION99.88
3.64-3.830.33621630.22771563X-RAY DIFFRACTION99.83
3.83-4.060.2791600.22591553X-RAY DIFFRACTION99.71
4.07-4.380.24161590.21031552X-RAY DIFFRACTION99.65
4.38-4.820.22921690.20551560X-RAY DIFFRACTION99.71
4.82-5.50.25131630.22451549X-RAY DIFFRACTION99.83
5.51-6.910.28021650.26921551X-RAY DIFFRACTION99.88
6.91-24.890.26891680.21261562X-RAY DIFFRACTION99.83

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