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- PDB-6vf7: DNA Polymerase Mu, 8-oxodGTP:At Ground State Ternary Complex, 50 ... -

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Basic information

Entry
Database: PDB / ID: 6vf7
TitleDNA Polymerase Mu, 8-oxodGTP:At Ground State Ternary Complex, 50 mM Mn2+ (15 min)
Components
  • DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*TP*A)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA-directed DNA/RNA polymerase mu
KeywordsREPLICATION / Time-Lapse Crystallography / Oxidized Ribonucleotide 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
8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.871 Å
AuthorsJamsen, J.A. / Wilson, S.H.
Funding support United States, Japan, 4items
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)Z01-10ES050161 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1K99ES029572-01 United States
Japan Society for the Promotion of Science (JSPS)16K16195 Japan
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for proficient oxidized ribonucleotide insertion in double strand break repair.
Authors: Jamsen, J.A. / Sassa, A. / Perera, L. / Shock, D.D. / Beard, W.A. / Wilson, S.H.
History
DepositionJan 3, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Sep 3, 2025Group: 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

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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*A)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,74219
Polymers45,1784
Non-polymers1,56415
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6800 Å2
ΔGint-58 kcal/mol
Surface area15750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.159, 68.927, 110.446
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) / 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.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*CP*GP*TP*A)-3')


Mass: 1190.830 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.) synthetic construct (others)

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Non-polymers , 7 types, 331 molecules

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


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-8DG / 8-OXO-2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION
#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-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
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.53 Å3/Da / Density % sol: 51.47 % / Mosaicity: 0.235 °
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: Mar 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→50 Å / Num. obs: 38515 / % possible obs: 99.5 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.045 / Rrim(I) all: 0.104 / Χ2: 1.028 / Net I/σ(I): 8.4 / Num. measured all: 194774
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.87-1.94.80.9318910.6050.4541.0381.03699.8
1.9-1.944.90.80118990.7240.3830.891.01499.9
1.94-1.9750.69518900.7870.3280.771.0499.5
1.97-2.0150.63218880.8090.2980.7011.08899.6
2.01-2.065.10.50619030.8740.2360.561.05199.7
2.06-2.115.10.43318990.9080.2030.4791.07799.8
2.11-2.165.20.34319290.9390.1580.3781.10199.9
2.16-2.225.10.30118990.9460.1410.3331.07499.8
2.22-2.284.90.25119200.9670.120.2791.09699.7
2.28-2.364.80.20818960.9680.1020.2321.0799.7
2.36-2.444.30.16918690.9740.0910.1931.08597.6
2.44-2.544.80.14319150.9860.070.161.05399.5
2.54-2.655.40.12819360.9890.0580.1411.05599.9
2.65-2.795.40.1119130.9920.050.1211.08299.8
2.79-2.975.40.08919410.9940.0420.0991.02399.4
2.97-3.25.40.07219350.9950.0340.081.00599.6
3.2-3.525.40.05519750.9970.0260.0610.943100
3.52-4.035.30.04819540.9970.0230.0540.90999.7
4.03-5.074.50.04319640.9970.0220.0490.85298.4
5.07-505.20.04620990.9970.0220.0510.93799.1

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M04

4m04


Resolution: 1.871→35.035 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1967 1921 5 %
Rwork0.1658 36536 -
obs0.1673 38457 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 89.83 Å2 / Biso mean: 30.6038 Å2 / Biso min: 9.58 Å2
Refinement stepCycle: final / Resolution: 1.871→35.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 344 59 322 3247
Biso mean--25.74 36.36 -
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 (%)
1.871-1.91760.27441360.23282548100
1.9176-1.96950.271380.21292587100
1.9695-2.02740.21811310.19952565100
2.0274-2.09280.22081360.18992580100
2.0928-2.16760.20771350.16762599100
2.1676-2.25440.22541350.16492566100
2.2544-2.3570.18551390.15732604100
2.357-2.48120.21521330.1542255698
2.4812-2.63660.18581380.162615100
2.6366-2.84010.20041370.1632604100
2.8401-3.12580.19321370.1692261999
3.1258-3.57770.17621390.15722655100
3.5777-4.5060.15741410.1392265699
4.506-35.0350.21361460.1802278299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7675-0.3768-0.22880.95860.16780.71610.11050.11940.1257-0.0222-0.0523-0.0696-0.00460.00840.00370.20630.00730.01090.19960.02110.16313.498-3.3905-9.8418
20.3391-0.0204-0.00520.2112-0.10010.04750.22080.563-0.0306-0.5276-0.15710.0003-0.1479-0.2160.00240.29790.0512-0.0010.3743-0.01790.1703-3.0076-6.3397-24.2508
30.01880.01530.00790.02320.00930.02070.13320.26780.1515-0.1594-0.03140.081-0.07390.17130.00020.28250.02240.04740.28720.08120.22653.04275.2718-18.0884
40.044-0.07150.03040.1178-0.0520.0250.05060.0382-0.2248-0.3391-0.07960.24890.2935-0.36290.00170.347-0.0052-0.07540.4631-0.11680.26543.3623-22.1045-25.9516
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 137 through 494)A137 - 494
2X-RAY DIFFRACTION2(chain 'T' and resid 1 through 9)T1 - 9
3X-RAY DIFFRACTION3(chain 'P' and resid 1 through 4)P1 - 4
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 4)D1 - 4

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