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- PDB-6d0m: Polymerase Eta post-insertion binary complex with cytarabine (AraC) -

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Basic information

Entry
Database: PDB / ID: 6d0m
TitlePolymerase Eta post-insertion binary complex with cytarabine (AraC)
Components
  • DNA (5'-D(*CP*AP*TP*GP*AP*CP*AP*GP*TP*GP*CP*T)-3')
  • DNA polymerase eta
  • DNA/RNA (5'-D(*AP*GP*CP*AP*CP*TP*GP*T)-R(P*(CAR))-3')
KeywordsTRANSFERASE/DNA / Cytarabine / AraC / DNA damage / Translesion / DNA synthesis / DNA Replication / TRANSFERASE / 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 / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain ...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 / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / 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 Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.832 Å
AuthorsRechkoblit, O. / Aggarwal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA200575 United States
CitationJournal: Sci Rep / Year: 2018
Title: Structural basis for polymerase eta-promoted resistance to the anticancer nucleoside analog cytarabine.
Authors: Rechkoblit, O. / Choudhury, J.R. / Buku, A. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionApr 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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

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Assembly

Deposited unit
A: DNA polymerase eta
T: DNA (5'-D(*CP*AP*TP*GP*AP*CP*AP*GP*TP*GP*CP*T)-3')
P: DNA/RNA (5'-D(*AP*GP*CP*AP*CP*TP*GP*T)-R(P*(CAR))-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1324
Polymers55,0403
Non-polymers921
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-31 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.566, 98.566, 81.477
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 48645.762 Da / Num. of mol.: 1 / Fragment: residues 1-432 / Mutation: C406M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLH, RAD30, RAD30A, XPV / Plasmid: PET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y253, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(*CP*AP*TP*GP*AP*CP*AP*GP*TP*GP*CP*T)-3')


Mass: 3662.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Engineered / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA/RNA (5'-D(*AP*GP*CP*AP*CP*TP*GP*T)-R(P*(CAR))-3')


Mass: 2731.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Engineered / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O

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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: 40.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES buffer, PEG1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Oct 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.83→45 Å / Num. obs: 39467 / % possible obs: 99.7 % / Redundancy: 12 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 31.4
Reflection shellResolution: 1.83→1.86 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 2.25 / Num. unique obs: 1849 / % possible all: 95.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J9P

4j9p


Resolution: 1.832→42.68 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1962 1977 5.01 %
Rwork0.1603 --
obs0.1621 39435 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.832→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3321 409 6 412 4148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063989
X-RAY DIFFRACTIONf_angle_d0.8255505
X-RAY DIFFRACTIONf_dihedral_angle_d20.6962388
X-RAY DIFFRACTIONf_chiral_restr0.047629
X-RAY DIFFRACTIONf_plane_restr0.005638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8316-1.87740.31611370.2612524X-RAY DIFFRACTION95
1.8774-1.92810.23311620.20252646X-RAY DIFFRACTION100
1.9281-1.98490.21661390.17482673X-RAY DIFFRACTION100
1.9849-2.04890.20671470.16712670X-RAY DIFFRACTION100
2.0489-2.12210.2191150.16562696X-RAY DIFFRACTION100
2.1221-2.20710.22311450.15642701X-RAY DIFFRACTION100
2.2071-2.30760.17381420.14882662X-RAY DIFFRACTION100
2.3076-2.42920.19071310.14782683X-RAY DIFFRACTION100
2.4292-2.58140.18041350.15642684X-RAY DIFFRACTION100
2.5814-2.78070.1791520.15532683X-RAY DIFFRACTION100
2.7807-3.06040.18781370.15832695X-RAY DIFFRACTION100
3.0604-3.50310.17531430.14762698X-RAY DIFFRACTION100
3.5031-4.41280.17921530.13642690X-RAY DIFFRACTION100
4.4128-42.69190.21181390.17922753X-RAY DIFFRACTION100

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