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- PDB-9dr9: Binary product complex of DNA polymerase iota with DNA -

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Basic information

Entry
Database: PDB / ID: 9dr9
TitleBinary product complex of DNA polymerase iota with DNA
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
DNA / DNA (> 10) / DNA polymerase iota
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 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
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')


Theoretical massNumber of molelcules
Total (without water)52,8332
Polymers52,8332
Non-polymers00
Water2,720151
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')

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')


Theoretical massNumber of molelcules
Total (without water)105,6664
Polymers105,6664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area9100 Å2
ΔGint-62 kcal/mol
Surface area37440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.100, 97.100, 202.044
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: in cystalo product DNA / Source: (synth.) Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
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: 2.6 Å3/Da / Density % sol: 52.73 %
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: Sep 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.06→48.55 Å / Num. obs: 28209 / % possible obs: 100 % / Redundancy: 18.9 % / Biso Wilson estimate: 35.9 Å2 / CC1/2: 1 / Rpim(I) all: 0.018 / Net I/σ(I): 25.8
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 11.6 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2057 / CC1/2: 0.766 / Rpim(I) all: 0.419 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
XDSdata reduction
XDSdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→43.76 Å / SU ML: 0.437 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 34.7555
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2972 1404 4.98 %
Rwork0.2549 26803 -
obs0.257 28207 97.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.04 Å2
Refinement stepCycle: LAST / Resolution: 2.21→43.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2896 350 0 151 3397
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01683327
X-RAY DIFFRACTIONf_angle_d1.83424560
X-RAY DIFFRACTIONf_chiral_restr0.0943531
X-RAY DIFFRACTIONf_plane_restr0.013527
X-RAY DIFFRACTIONf_dihedral_angle_d15.6179562
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.21-2.290.63811100.55761947X-RAY DIFFRACTION73.28
2.29-2.380.35621420.33572694X-RAY DIFFRACTION99.86
2.38-2.490.30511350.29022710X-RAY DIFFRACTION99.96
2.49-2.620.3331400.26872707X-RAY DIFFRACTION100
2.62-2.780.30071470.28662705X-RAY DIFFRACTION99.96
2.78-30.3651380.30322732X-RAY DIFFRACTION99.97
3-3.30.30271430.25792751X-RAY DIFFRACTION100
3.3-3.780.28691380.24192754X-RAY DIFFRACTION99.21
3.78-4.760.24091450.19952815X-RAY DIFFRACTION99.97
4.76-43.760.25621660.22192988X-RAY DIFFRACTION99.68

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