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- PDB-7ktn: DNA Polymerase Mu, 8-oxodGTP:At Product State Ternary Complex, 10... -

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Basic information

Entry
Database: PDB / ID: 7ktn
TitleDNA Polymerase Mu, 8-oxodGTP:At Product State Ternary Complex, 10 mM Mg2+ (2160min)
Components
  • DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA-directed DNA/RNA polymerase mu
KeywordsREPLICATION / Time-Lapse Crystallography / Oxidized Nucleotide Insertion / DNA Polymerase Mu / Double Strand Break Repair
Function / homology
Function and homology information


somatic hypermutation of immunoglobulin genes / B cell differentiation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family ...DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
2,3-DIHYDROXY-1,4-DITHIOBUTANE / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsJamsen, J.A. / Wilson, S.H.
Funding support United States, Japan, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES050158 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01-ES050161 United States
Japan Society for the Promotion of Science (JSPS)16K16195 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Watching a double strand break repair polymerase insert a pro-mutagenic oxidized nucleotide.
Authors: Jamsen, J.A. / Sassa, A. / Shock, D.D. / Beard, W.A. / Wilson, S.H.
History
DepositionNov 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 6, 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
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed DNA/RNA polymerase mu
T: DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
P: DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,20813
Polymers45,5234
Non-polymers6849
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-49 kcal/mol
Surface area16030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.229, 68.293, 111.412
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA-directed DNA/RNA polymerase mu / Pol Mu / Terminal transferase


Mass: 40054.434 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Plasmid: pGEXM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NP87, DNA-directed DNA polymerase

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DNA chain , 3 types, 3 molecules TPD

#2: DNA chain DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')


Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*CP*GP*TP*AP*(8OG))-3')


Mass: 1536.036 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA (5'-D(P*GP*CP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 7 types, 486 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.13 % / Mosaicity: 0.097 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 85-90mM HEPES pH 7.5, 17-18% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 104884 / % possible obs: 98.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.048 / Rrim(I) all: 0.114 / Χ2: 1.12 / Net I/σ(I): 14 / Num. measured all: 583554
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.33-1.353.90.49746100.8080.270.571.05288.4
1.35-1.384.50.44350140.8630.2280.5011.09795.1
1.38-1.45.40.39852390.9010.1880.4421.12599.9
1.4-1.435.90.34552650.9360.1560.3791.154100
1.43-1.465.90.29552080.9530.1320.3241.195100
1.46-1.55.90.24752460.9640.1110.2721.217100
1.5-1.545.90.20752460.9720.0940.2271.23399.9
1.54-1.585.70.17652440.9770.080.1941.23899.9
1.58-1.625.60.15252520.9810.070.1681.23499.9
1.62-1.685.10.13152470.9810.0630.1461.18199.4
1.68-1.745.60.12352210.9830.0560.1361.16799.5
1.74-1.816.10.11652590.9860.0520.1281.10499.9
1.81-1.8960.1153130.9870.0490.121.13899.9
1.89-1.995.90.10552650.9870.0470.1151.058100
1.99-2.115.70.153080.9860.0460.111.06699.9
2.11-2.275.40.09653220.9850.0450.1061.03299.6
2.27-2.55.40.09452610.9860.0430.1031.03198.8
2.5-2.876.20.09853920.9870.0430.1071.091100
2.87-3.615.90.09653740.9860.0440.1060.99299.5
3.61-505.30.10155980.9740.0480.1120.95398.9

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.15.2-3472refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M04

4m04


Resolution: 1.33→35.086 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1626 5247 5.01 %
Rwork0.1414 99549 -
obs0.1425 104796 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.48 Å2 / Biso mean: 21.7684 Å2 / Biso min: 9.53 Å2
Refinement stepCycle: final / Resolution: 1.33→35.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 367 21 485 3417
Biso mean--25.15 32.85 -
Num. residues----343
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3301-1.34530.23511570.2102284985
1.3453-1.36110.23331590.1898301791
1.3611-1.37770.22541710.1694318896
1.3777-1.39510.18441740.15633313100
1.3951-1.41350.18741720.14113292100
1.4135-1.43280.16531770.13713360100
1.4328-1.45330.16011740.13253319100
1.4533-1.4750.15431740.13083304100
1.475-1.49810.15711750.12173321100
1.4981-1.52260.16271760.11493323100
1.5226-1.54890.14581760.10873338100
1.5489-1.5770.12041740.10733306100
1.577-1.60740.13771750.10843333100
1.6074-1.64020.1471760.10633332100
1.6402-1.67580.13981720.1101331499
1.6758-1.71480.15531770.1096333299
1.7148-1.75770.13861750.1123324100
1.7577-1.80520.14041750.11593329100
1.8052-1.85840.14691770.11753360100
1.8584-1.91830.15131780.1253317100
1.9183-1.98690.16741820.13383354100
1.9869-2.06640.17481750.13673378100
2.0664-2.16050.14831740.13173359100
2.1605-2.27440.14521710.13443369100
2.2744-2.41680.15871760.127330798
2.4168-2.60340.15041800.13553384100
2.6034-2.86520.16141800.1493416100
2.8652-3.27960.17881780.15713413100
3.2796-4.13090.14741780.14523432100
4.1309-35.0860.19871890.1803356699

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