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- PDB-8v7g: Human DNA polymerase eta-DNA-gemC-ended primer-dAMPNPP ternary co... -

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Basic information

Entry
Database: PDB / ID: 8v7g
TitleHuman DNA polymerase eta-DNA-gemC-ended primer-dAMPNPP ternary complex with Mg2+
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*(U7B))-3')
  • DNA (5'-D(*CP*AP*TP*TP*GP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
KeywordsTransferase/DNA / DNA polymerase eta / 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 / response to radiation ...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 / response to radiation / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / site of double-strand break / damaged DNA binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / DNA repair / nucleoplasm / metal ion binding / nucleus / 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
Chem-DZ4 / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsChang, C. / Gao, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
Cancer Prevention and Research Institute of Texas (CPRIT)RR190046 United States
Welch FoundationC-2033-20200401 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM008280 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Sugar ring alignment and dynamics underline cytarabine and gemcitabine inhibition on Pol eta catalyzed DNA synthesis.
Authors: Chang, C. / Zhou, G. / Lee Luo, C. / Eleraky, S. / Moradi, M. / Gao, Y.
History
DepositionDec 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification
Revision 1.2Jun 4, 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 eta
T: DNA (5'-D(*CP*AP*TP*TP*GP*TP*GP*AP*CP*GP*CP*T)-3')
P: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*(U7B))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3507
Polymers54,7193
Non-polymers6314
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-44 kcal/mol
Surface area21840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.360, 98.360, 82.047
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 BL21(DE3) (bacteria) / References: UniProt: Q9Y253, DNA-directed DNA polymerase

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DNA chain , 2 types, 2 molecules TP

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


Mass: 3653.390 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*(U7B))-3')


Mass: 2447.587 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 328 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DZ4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 490.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O11P3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 2000MME, 0.1 M MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.9765 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Oct 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 1.52→42.59 Å / Num. obs: 69693 / % possible obs: 99.6 % / Redundancy: 9.9 % / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rrim(I) all: 0.042 / Net I/σ(I): 23.93
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.52-1.610.55218130.7680.6311
1.61-1.720.356209460.9190.3971
1.72-1.860.202195850.9730.2261
1.86-2.030.108178800.9920.1211
2.03-2.270.061161960.9970.0681
2.27-2.620.04143210.9990.0441
2.62-3.210.026120690.9990.0291
3.21-4.520.018934810.021
4.52-42.590.017519010.0191

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XSCALEdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→42.59 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1984 3473 4.98 %
Rwork0.1842 --
obs0.1849 69692 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 380 38 324 4056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083966
X-RAY DIFFRACTIONf_angle_d1.0815474
X-RAY DIFFRACTIONf_dihedral_angle_d19.2891522
X-RAY DIFFRACTIONf_chiral_restr0.061612
X-RAY DIFFRACTIONf_plane_restr0.009638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.540.25581300.22872470X-RAY DIFFRACTION93
1.54-1.560.24481230.22412652X-RAY DIFFRACTION100
1.56-1.580.23721300.21292630X-RAY DIFFRACTION100
1.58-1.610.2491570.20692645X-RAY DIFFRACTION100
1.61-1.630.21781190.21372645X-RAY DIFFRACTION100
1.63-1.660.23881170.20762659X-RAY DIFFRACTION100
1.66-1.690.26671320.21192690X-RAY DIFFRACTION100
1.69-1.720.23711190.21472647X-RAY DIFFRACTION100
1.72-1.760.21691190.20292685X-RAY DIFFRACTION100
1.76-1.80.22431690.2072608X-RAY DIFFRACTION100
1.8-1.840.20091480.20732627X-RAY DIFFRACTION100
1.84-1.880.22871360.19812666X-RAY DIFFRACTION100
1.88-1.940.2371280.20172691X-RAY DIFFRACTION100
1.94-1.990.2091530.1952619X-RAY DIFFRACTION100
1.99-2.060.25371550.20922638X-RAY DIFFRACTION100
2.06-2.130.21471480.19512645X-RAY DIFFRACTION100
2.13-2.220.20621580.19222620X-RAY DIFFRACTION100
2.22-2.320.21761510.19082631X-RAY DIFFRACTION100
2.32-2.440.22631700.18962640X-RAY DIFFRACTION100
2.44-2.590.22271300.20272676X-RAY DIFFRACTION100
2.59-2.790.20661260.19412674X-RAY DIFFRACTION100
2.79-3.070.20041440.19072658X-RAY DIFFRACTION100
3.07-3.520.17671480.17112670X-RAY DIFFRACTION100
3.52-4.430.1391360.14852695X-RAY DIFFRACTION100
4.43-42.590.16031270.1592738X-RAY DIFFRACTION100

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