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- PDB-7m7q: Human DNA Pol eta S113A with dT-ended primer and dAMPNPP -

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Basic information

Entry
Database: PDB / ID: 7m7q
TitleHuman DNA Pol eta S113A with dT-ended primer and dAMPNPP
Components
  • DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3')
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / DNA polymerase / Time resolved crystallography / deprotonation / 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
Chem-DZ4 / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.27 Å
AuthorsGregory, M.T. / Gao, Y. / Yang, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK036146 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Multiple deprotonation paths of the nucleophile 3'-OH in the DNA synthesis reaction.
Authors: Gregory, M.T. / Gao, Y. / Cui, Q. / Yang, W.
History
DepositionMar 28, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*AP*TP*GP*AP*CP*GP*CP*T)-3')
P: DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1839
Polymers54,9703
Non-polymers1,2136
Water6,936385
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-47 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.927, 98.927, 81.807
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 48601.707 Da / Num. of mol.: 1 / Mutation: S113A
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(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')


Mass: 3637.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*AP*GP*CP*GP*TP*CP*AP*T)-3')


Mass: 2730.810 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 391 molecules

#4: Chemical ChemComp-DZ4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine


Mass: 490.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O11P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.1 Å3/Da / Density % sol: 41.47 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6 / Details: 15% PEG 2000 MME, 100 mM MES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.27→35 Å / Num. obs: 20884 / % possible obs: 98.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.154 / Χ2: 1.018 / Net I/σ(I): 5.9 / Num. measured all: 80413
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.27-2.313.70.68610601.079199.9
2.31-2.353.80.52510571.021199.9
2.35-2.43.80.49110421.031199.9
2.4-2.453.80.49610561.032199.8
2.45-2.53.80.49110611.029199.7
2.5-2.563.80.42910531.055199.7
2.56-2.623.80.36910550.996199.5
2.62-2.693.80.35110361.052199.3
2.69-2.773.80.28410391.029199.3
2.77-2.863.80.25910711.02199.4
2.86-2.963.80.23910320.947199.2
2.96-3.083.90.19310611.018198.9
3.08-3.223.80.15210481.026198.8
3.22-3.393.90.12410520.996198.2
3.39-3.63.90.12210220.985198.1
3.6-3.883.90.12110350.971197.5
3.88-4.273.90.08210391.001196.7
4.27-4.893.90.07510261.026196.2
4.89-6.1540.05810271195
6.15-3540.03210121.039191.7

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4ecq

4ecq


Resolution: 2.27→32.38 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 1602 7.69 %
Rwork0.169 19229 -
obs0.1732 20831 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 100.64 Å2 / Biso mean: 25.4911 Å2 / Biso min: 7.55 Å2
Refinement stepCycle: final / Resolution: 2.27→32.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3337 391 55 385 4168
Biso mean--26.65 29.5 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013991
X-RAY DIFFRACTIONf_angle_d1.3235479
X-RAY DIFFRACTIONf_dihedral_angle_d25.1381582
X-RAY DIFFRACTIONf_chiral_restr0.069609
X-RAY DIFFRACTIONf_plane_restr0.008637
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.27-2.340.33091290.22271783191299
2.34-2.420.26381620.204117501912100
2.42-2.520.29261750.197317401915100
2.52-2.630.26221510.195217551906100
2.64-2.770.25741450.18881741188699
2.77-2.950.24311360.18571773190999
2.95-3.170.21340.16921770190499
3.17-3.490.21541410.14951756189798
3.49-40.20251510.14361723187498
4-5.030.17621320.1451745187796
5.04-32.380.19361460.16391693183993

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