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- PDB-7u7l: Human DNA polymerase eta-DNA ternary mismatch complex:reaction wi... -

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Basic information

Entry
Database: PDB / ID: 7u7l
TitleHuman DNA polymerase eta-DNA ternary mismatch complex:reaction with 1.0 mM Mg2+ for 300s with flipped-out product
Components
  • DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*G)-3')
  • DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3')
  • DNA polymerase eta
KeywordsTRANSFERASE/DNA / Polymerase / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


response to UV-C / DNA synthesis involved in DNA repair / error-free translesion synthesis / 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 / DNA synthesis involved in DNA repair / error-free translesion synthesis / 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 / DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNApol eta/Rev1, HhH motif / 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. ...Ubiquitin-Binding Zinc Finger / DNA polymerase eta, ubiquitin-binding zinc finger / Zinc finger UBZ3-type profile. / DNApol eta/Rev1, HhH motif / 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
DIPHOSPHATE / DNA / DNA (> 10) / DNA polymerase eta
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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)T32GM008280 United States
CitationJournal: Nat Commun / Year: 2022
Title: In crystallo observation of three metal ion promoted DNA polymerase misincorporation.
Authors: Chang, C. / Lee Luo, C. / Gao, Y.
History
DepositionMar 7, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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 (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4858
Polymers55,0113
Non-polymers4755
Water8,017445
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-40 kcal/mol
Surface area22340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.164, 98.164, 81.882
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 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*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 chain DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*G)-3')


Mass: 2755.823 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 450 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-DPO / DIPHOSPHATE / Pyrophosphate


Mass: 173.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O7P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / 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: 40.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 10% 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-F / Wavelength: 0.9787 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 31, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.47→42.1 Å / Num. obs: 75884 / % possible obs: 99 % / Redundancy: 4.929 % / Biso Wilson estimate: 19.94 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.052 / Χ2: 0.932 / Net I/σ(I): 16.23 / Num. measured all: 731442
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
1.47-1.562.3640.6081.295520224299233480.5520.77596.1
1.56-1.673.9970.3992.988987522708224840.8480.46199
1.67-1.85.7170.2456.412077421271211250.9660.26999.3
1.8-1.975.7740.1311.7811199019501193940.9910.14399.5
1.97-2.25.7610.07619.9810130217645175830.9960.08399.6
2.2-2.555.7340.05327.978920015590155550.9980.05899.8
2.55-3.125.6680.04235.297425913114131020.9980.04699.9
3.12-4.45.6260.03443.425733010192101910.9990.037100
4.4-42.15.6280.03445.8431510560855990.9990.03799.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ECQ

4ecq


Resolution: 1.47→42.1 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1936 3834 5.05 %
Rwork0.1871 72042 -
obs0.1874 75876 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.44 Å2 / Biso mean: 26.3343 Å2 / Biso min: 11.29 Å2
Refinement stepCycle: final / Resolution: 1.47→42.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 409 28 445 4248
Biso mean--29.3 32.64 -
Num. residues----450
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.47-1.490.30961320.30182594272697
1.49-1.510.25391230.272126712794100
1.51-1.530.27221440.255626362780100
1.53-1.550.24851550.246326302785100
1.55-1.570.25361420.229127172859100
1.57-1.60.22371340.220826352769100
1.6-1.630.22911540.217626482802100
1.63-1.650.22361520.209926482800100
1.65-1.680.19861400.214926802820100
1.68-1.720.26831350.222826742809100
1.72-1.750.22031400.216626682808100
1.75-1.790.2451460.211426552801100
1.79-1.830.24061450.207826612806100
1.83-1.880.21381300.209826742804100
1.88-1.930.19111490.203426522801100
1.93-1.980.19531460.194226662812100
1.98-2.050.22541480.201126782826100
2.05-2.120.2041620.195526392801100
2.12-2.210.19121510.18726592810100
2.21-2.310.18541600.183526522812100
2.31-2.430.21371100.192527092819100
2.43-2.580.2091520.20426812833100
2.58-2.780.2211420.194326762818100
2.78-3.060.19671550.196526652820100
3.06-3.50.17631210.169227062827100
3.5-4.410.15481170.148827322849100
4.41-42.10.14771490.165427362885100

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