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- PDB-7m7l: Human DNA Pol eta with dA-ended primer and dAMPNPP -

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Basic information

Entry
Database: PDB / ID: 7m7l
TitleHuman DNA Pol eta with dA-ended primer and dAMPNPP
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*A)-3')
  • DNA (5'-D(*CP*AP*TP*TP*TP*TP*GP*AP*CP*GP*CP*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-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
Chem-DZ4 / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.58 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*TP*TP*GP*AP*CP*GP*CP*T)-3')
P: DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,8038
Polymers54,6823
Non-polymers1,1215
Water8,755486
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-40 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.645, 98.645, 81.990
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: 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(*CP*AP*TP*TP*TP*TP*GP*AP*CP*GP*CP*T)-3')


Mass: 3628.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*A)-3')


Mass: 2435.631 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 491 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 6 / Details: 15% PEG 3350, 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 31, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→30.04 Å / Num. obs: 62075 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.7
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 6106

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Processing

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

4ecq


Resolution: 1.58→30.04 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 4805 7.74 %
Rwork0.1751 57270 -
obs0.178 62075 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.69 Å2 / Biso mean: 21.1566 Å2 / Biso min: 4.86 Å2
Refinement stepCycle: final / Resolution: 1.58→30.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 387 49 486 4231
Biso mean--17.95 30.2 -
Num. residues----447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064045
X-RAY DIFFRACTIONf_angle_d0.9215574
X-RAY DIFFRACTIONf_dihedral_angle_d25.9781595
X-RAY DIFFRACTIONf_chiral_restr0.052627
X-RAY DIFFRACTIONf_plane_restr0.005653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.58-1.60.26041490.21751859200897
1.6-1.610.23771680.21291881204999
1.61-1.630.2561560.218118932049100
1.63-1.660.23211620.206518872049100
1.66-1.680.23371670.207819452112100
1.68-1.70.26841540.217218872041100
1.7-1.720.24851830.216118832066100
1.72-1.750.23371700.199918912061100
1.75-1.780.26141420.201219142056100
1.78-1.810.25251610.200619272088100
1.81-1.840.23081630.194219152078100
1.84-1.870.2681810.190818562037100
1.87-1.910.23571580.185919232081100
1.91-1.950.22891500.184819282078100
1.95-1.990.23451530.17719052058100
1.99-2.030.21590.191719212080100
2.03-2.090.21621680.182619012069100
2.09-2.140.23631370.173619392076100
2.14-2.20.20391610.167619052066100
2.2-2.280.22511660.171119032069100
2.28-2.360.2281420.169819352077100
2.36-2.450.22441780.171518832061100
2.45-2.560.21481830.186819082091100
2.56-2.70.21291540.178419072061100
2.7-2.870.22961550.176719382093100
2.87-3.090.20871560.17719342090100
3.09-3.40.21381450.160319372082100
3.4-3.890.17181760.142419172093100
3.89-4.90.14941440.140919452089100
4.9-30.040.20751640.1821903206797

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