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- PDB-8v7h: Human DNA polymerase eta-DNA-araC-ended primer ternary complex:gr... -

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Basic information

Entry
Database: PDB / ID: 8v7h
TitleHuman DNA polymerase eta-DNA-araC-ended primer ternary complex:ground state at pH7.0 (K+ MES) with 1 Ca2+ ion
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*A)-R(P*(CAR))-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 / 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-directed DNA polymerase / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / DNA repair / zinc ion binding / nucleoplasm / 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
2'-DEOXYADENOSINE 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: 1.68 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*A)-R(P*(CAR))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2696
Polymers54,6993
Non-polymers5703
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5530 Å2
ΔGint-43 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.403, 98.403, 81.574
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*A)-R(P*(CAR))-3')


Mass: 2427.606 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 80 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.08 Å3/Da / Density % sol: 40.99 %
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: APS / Beamline: 21-ID-D / Wavelength: 1.12723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 1.68→37.77 Å / Num. obs: 50730 / % possible obs: 100 % / Redundancy: 20.4 % / CC1/2: 1 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.048 / Net I/σ(I): 25.27
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.68-1.790.819161150.8580.8621
1.79-1.910.454152090.950.4781
1.91-2.060.236141420.9860.251
2.06-2.260.126129760.9960.1331
2.26-2.520.077117740.9980.0811
2.52-2.910.053104110.9990.0551
2.91-3.570.03787490.9990.0391
3.57-5.030.029677410.031
5.03-37.770.02737570.9990.0291

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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: 1.68→37.77 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 2413 4.76 %
Rwork0.2081 --
obs0.2093 50723 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.68→37.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 379 32 77 3797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083985
X-RAY DIFFRACTIONf_angle_d1.1395493
X-RAY DIFFRACTIONf_dihedral_angle_d19.9481536
X-RAY DIFFRACTIONf_chiral_restr0.069619
X-RAY DIFFRACTIONf_plane_restr0.009634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.720.35811270.31032810X-RAY DIFFRACTION100
1.72-1.760.33671230.28912865X-RAY DIFFRACTION100
1.76-1.80.30641700.25732817X-RAY DIFFRACTION100
1.8-1.840.29241260.2462813X-RAY DIFFRACTION100
1.84-1.890.28191270.24262854X-RAY DIFFRACTION100
1.89-1.950.28331150.24222837X-RAY DIFFRACTION100
1.95-2.010.26991580.24132851X-RAY DIFFRACTION100
2.01-2.080.30911480.25072806X-RAY DIFFRACTION100
2.08-2.170.27191380.24412869X-RAY DIFFRACTION100
2.17-2.260.28931670.23372789X-RAY DIFFRACTION100
2.26-2.380.2811420.2272853X-RAY DIFFRACTION100
2.38-2.530.2791340.24632850X-RAY DIFFRACTION100
2.53-2.730.26311620.23662851X-RAY DIFFRACTION100
2.73-30.26221470.2422813X-RAY DIFFRACTION100
3-3.440.21731510.20712850X-RAY DIFFRACTION100
3.44-4.330.19891420.17352872X-RAY DIFFRACTION100
4.33-37.770.15521360.15592910X-RAY DIFFRACTION100

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