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- PDB-8evf: HUMAN DNA POLYMERASE ETA EXTENSION COMPLEX WITH AN INCOMING DCTP -

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Basic information

Entry
Database: PDB / ID: 8evf
TitleHUMAN DNA POLYMERASE ETA EXTENSION COMPLEX WITH AN INCOMING DCTP
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*G)-3')
  • DNA 5'-D(P*TP*GP*(MO1)P*TP*GP*AP*CP*GP*CP*T-3'
  • DNA polymerase eta
KeywordsREPLICATION / TRANSFERASE/DNA / DNA DAMAGE / DNA POLYMERASE / LESION BYPASS / Y-FAMILY POLYMERASE / TRANSLESION DNA SYNTHESIS (TLS) / DNA BINDING PROTEIN / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH ...response to UV-C / error-free translesion synthesis / DNA synthesis involved in DNA repair / cellular response to UV-C / pyrimidine dimer repair / error-prone translesion synthesis / regulation of DNA repair / replication fork / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / response to radiation / HDR through Homologous Recombination (HRR) / site of double-strand break / DNA replication / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA repair / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / 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 ...Ubiquitin-Binding Zinc Finger / DNApol eta/Rev1, HhH motif / DNA polymerase eta, ubiquitin-binding zinc finger / : / Zinc finger UBZ3-type profile. / 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
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.87 Å
AuthorsPallan, P.S. / Egli, M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01 CA-87819 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01 CA-160032 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: The peroxidation-derived DNA adduct, 6-oxo-M 1 dG, is a strong block to replication by human DNA polymerase eta.
Authors: Richie-Jannetta, R. / Pallan, P. / Kingsley, P.J. / Kamdar, N. / Egli, M. / Marnett, L.J.
History
DepositionOct 20, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA polymerase eta
T: DNA 5'-D(P*TP*GP*(MO1)P*TP*GP*AP*CP*GP*CP*T-3'
P: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3476
Polymers54,8003
Non-polymers5473
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-48 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.671, 98.671, 81.736
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase eta / RAD30 homolog A / Xeroderma pigmentosum variant type protein


Mass: 48617.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, RAD30, RAD30A, XPV / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y253, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

#2: DNA chain DNA 5'-D(P*TP*GP*(MO1)P*TP*GP*AP*CP*GP*CP*T-3'


Mass: 3730.435 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*G)-3')


Mass: 2451.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 26 molecules

#4: Chemical ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#5: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M MES PH 5.5, 5mM calcium chloride, 15-22% PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 17, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 2.87→30 Å / Num. obs: 10308 / % possible obs: 98.5 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.049 / Net I/σ(I): 15.68
Reflection shellResolution: 2.87→2.92 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 536 / % possible all: 99.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L1I

5l1i


Resolution: 2.87→29.53 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 471 4.58 %
Rwork0.2042 --
obs0.2063 10282 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.87→29.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3225 374 30 23 3652
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043727
X-RAY DIFFRACTIONf_angle_d0.7455114
X-RAY DIFFRACTIONf_dihedral_angle_d18.222620
X-RAY DIFFRACTIONf_chiral_restr0.043573
X-RAY DIFFRACTIONf_plane_restr0.005589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.87-3.280.33171520.2623295X-RAY DIFFRACTION99
3.28-4.140.26181610.20153244X-RAY DIFFRACTION99
4.14-29.530.21921580.18583272X-RAY DIFFRACTION98

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