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- PDB-8v7k: Human DNA polymerase eta-DNA-araC-ended primer ternary complex:re... -

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Basic information

Entry
Database: PDB / ID: 8v7k
TitleHuman DNA polymerase eta-DNA-araC-ended primer ternary complex:reaction with 10 mM Mn2+ for 1800s
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 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
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: 1.65 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: To Be Published
Title: Human DNA polymerase eta-DNA-araC-ended primer ternary complex:reaction with 10 mM Mn2+ for 1800s
Authors: Chang, C. / Gao, Y.
History
DepositionDec 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2024Provider: repository / Type: Initial release

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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*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)55,3006
Polymers54,6993
Non-polymers6013
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-41 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.520, 98.520, 81.652
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 , 3 types, 109 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.09 Å3/Da / Density % sol: 41.19 %
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: 1.1272 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 17, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1272 Å / Relative weight: 1
ReflectionResolution: 1.65→37.81 Å / Num. obs: 53654 / % possible obs: 99.9 % / Redundancy: 20.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.068 / Net I/σ(I): 19.33
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.65-1.750.869170390.8140.9161
1.75-1.880.503160890.9350.531
1.88-2.030.281149570.9790.2971
2.03-2.220.15137560.9920.1581
2.22-2.480.097124590.9970.1011
2.48-2.860.072109620.9980.0751
2.86-3.50.05393030.9990.0561
3.5-4.940.04371750.9990.0451
4.94-37.810.03539580.9990.0371

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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: 1.65→37.81 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2328 2615 4.87 %
Rwork0.2056 --
obs0.2069 53650 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 379 32 106 3826
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123995
X-RAY DIFFRACTIONf_angle_d1.3215507
X-RAY DIFFRACTIONf_dihedral_angle_d19.8171541
X-RAY DIFFRACTIONf_chiral_restr0.076620
X-RAY DIFFRACTIONf_plane_restr0.008635
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.680.25411220.24042663X-RAY DIFFRACTION99
1.68-1.720.26111510.22412637X-RAY DIFFRACTION100
1.72-1.750.37421280.25312716X-RAY DIFFRACTION100
1.75-1.790.31221360.25092665X-RAY DIFFRACTION100
1.79-1.830.24831300.24082687X-RAY DIFFRACTION100
1.83-1.880.2641380.22782671X-RAY DIFFRACTION100
1.88-1.930.2461490.2232666X-RAY DIFFRACTION100
1.93-1.990.251500.21872672X-RAY DIFFRACTION100
1.99-2.050.26761420.22922678X-RAY DIFFRACTION100
2.05-2.120.23881690.22072633X-RAY DIFFRACTION100
2.12-2.210.2631320.22762713X-RAY DIFFRACTION100
2.21-2.310.27161420.21722670X-RAY DIFFRACTION100
2.31-2.430.24561440.22122663X-RAY DIFFRACTION100
2.43-2.580.24541360.23412710X-RAY DIFFRACTION100
2.58-2.780.25381400.21922689X-RAY DIFFRACTION100
2.78-3.060.23341310.2332695X-RAY DIFFRACTION100
3.06-3.50.23811160.19882729X-RAY DIFFRACTION100
3.5-4.410.19661220.17232724X-RAY DIFFRACTION100
4.41-37.810.18451370.17282754X-RAY DIFFRACTION100

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