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- PDB-8e8b: Human DNA polymerase eta-DNA-rU-ended primer ternary mismatch com... -

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Basic information

Entry
Database: PDB / ID: 8e8b
TitleHuman DNA polymerase eta-DNA-rU-ended primer ternary mismatch complex:ground state at pH7.0 (K+ MES) with 1 Ca2+ ion
Components
  • DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
  • DNA/RNA (5'-D(*AP*GP*CP*GP*TP*CP*A)-R(P*U)-3')
KeywordsTRANSFERASE/DNA / DNA polymerase / 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 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'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / : / DNA / DNA (> 10) / DNA/RNA hybrid / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChang, C. / Gao, Y.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32GM008280 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR190046 United States
Welch FoundationC-2033-20200401 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase eta and reduces DNA synthesis fidelity.
Authors: Chang, C. / Lee Luo, C. / Eleraky, S. / Lin, A. / Zhou, G. / Gao, Y.
History
DepositionAug 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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/RNA (5'-D(*AP*GP*CP*GP*TP*CP*A)-R(P*U)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,2706
Polymers54,6843
Non-polymers5863
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-41 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.870, 97.870, 82.130
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 / DNA chain / DNA/RNA hybrid , 3 types, 3 molecules ATP

#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
#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.) synthetic construct (others)
#3: DNA/RNA hybrid DNA/RNA (5'-D(*AP*GP*CP*GP*TP*CP*A)-R(P*U)-3')


Mass: 2428.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 43 molecules

#4: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.07 Å3/Da / Density % sol: 40.66 %
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: 0.97618 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97618 Å / Relative weight: 1
ReflectionResolution: 2.02→32.04 Å / Num. obs: 50583 / % possible obs: 87.5 % / Redundancy: 10.46 % / Biso Wilson estimate: 37.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.084 / Χ2: 0.911 / Net I/σ(I): 17.13 / Num. measured all: 529123 / Scaling rejects: 24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.02-2.074.6180.8141.75731429612410.6480.90828.9
2.07-2.136.1460.7272.4115653420425470.7450.79360.6
2.13-2.196.9250.5863.2719038398927490.8480.63368.9
2.19-2.267.560.494.1123359391030900.8920.52679
2.26-2.338.2040.4145.1329215387635610.9170.44291.9
2.33-2.4110.4990.3616.7938047368936240.9630.37998.2
2.41-2.510.9810.312838960355535480.9760.32799.8
2.5-2.6111.0060.2589.5237419340234000.9820.27199.9
2.61-2.7210.8730.19811.8636032331633140.9890.20799.9
2.72-2.8610.7430.15814.3733528312431210.9930.16699.9
2.86-3.0110.5720.13116.7831462297629760.9950.138100
3.01-3.1910.2630.10320.7929218284728470.9960.108100
3.19-3.419.1680.07824.6623874262926040.9970.08399
3.41-3.6910.9810.0730.6827034246524620.9980.07499.9
3.69-4.0411.3520.06434.725826227522750.9980.067100
4.04-4.5116.390.06442.7133633205220520.9990.066100
4.51-5.2116.0620.06244.328959180318030.9990.064100
5.21-6.3815.0080.05942.2823247154915490.9990.061100
6.38-9.0316.0860.05347.0919078118611860.9990.054100
9.03-32.0415.4730.04950.498106386340.9990.0599.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7M7L

7m7l


Resolution: 2.2→32.04 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 28.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2432 1187 5.33 %
Rwork0.1949 21069 -
obs0.1976 22256 97.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113 Å2 / Biso mean: 42.5509 Å2 / Biso min: 19.86 Å2
Refinement stepCycle: final / Resolution: 2.2→32.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 378 33 40 3760
Biso mean--48.05 37.13 -
Num. residues----445
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.30.29151280.22082252238084
2.3-2.420.2981480.22312651279999
2.42-2.570.33881530.251826692822100
2.57-2.770.37051430.251227082851100
2.77-3.050.35391360.24526982834100
3.05-3.490.261640.20722652281699
3.49-4.40.18341560.165827032859100
4.4-32.040.19051590.156927362895100

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