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- PDB-8e89: Human DNA polymerase eta-DNA-rU-ended primer-binary complex -

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Basic information

Entry
Database: PDB / ID: 8.0E+89
TitleHuman DNA polymerase eta-DNA-rU-ended primer-binary complex
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 / response to radiation ...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 / response to radiation / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / site of double-strand break / damaged DNA binding / DNA-directed DNA polymerase / 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/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')


Theoretical massNumber of molelcules
Total (without water)54,6843
Polymers54,6843
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4080 Å2
ΔGint-29 kcal/mol
Surface area21260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.394, 97.394, 80.911
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 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)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.02 Å3/Da / Density % sol: 39.18 %
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: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 2.2→37.4 Å / Num. obs: 43810 / % possible obs: 99.8 % / Redundancy: 10.314 % / Biso Wilson estimate: 48.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.085 / Χ2: 0.767 / Net I/σ(I): 15.8 / Num. measured all: 451872
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
2.2-2.3310.7620.8532.0175765711070400.8390.89699
2.33-2.4910.7750.5663.3471805666466640.9320.595100
2.49-2.6910.4980.3825.3465096620162010.9680.402100
2.69-2.949.3330.2438.6153115569156910.9820.258100
2.94-3.2910.7070.13217.2555150515151510.9960.139100
3.29-3.7910.2340.0828.6746822457545750.9970.085100
3.79-4.649.8220.0638.4237756384438440.9980.063100
4.64-6.539.3140.05140.6727764298129810.9980.054100
6.53-37.411.1840.03650.9918599166716630.9990.03899.8

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Processing

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

7m7l


Resolution: 2.2→37.4 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2617 1183 5.3 %
Rwork0.2006 21158 -
obs0.2038 22341 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.88 Å2 / Biso mean: 54.2812 Å2 / Biso min: 31.42 Å2
Refinement stepCycle: final / Resolution: 2.2→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 378 0 12 3699
Biso mean---48.98 -
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 (%)
2.2-2.290.33361590.24462583274299
2.3-2.420.30481640.226926162780100
2.42-2.570.3171420.263826562798100
2.57-2.760.30521460.236226292775100
2.77-3.040.36511210.271826772798100
3.04-3.480.28091450.221526472792100
3.48-4.390.24271650.18626402805100
4.39-37.40.21661410.159127102851100

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