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- PDB-6vf9: DNA Polymerase Mu, 8-oxorGTP:Ct Ternary Complex, 50 mM Mg2+ (2160 min) -

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Basic information

Entry
Database: PDB / ID: 6vf9
TitleDNA Polymerase Mu, 8-oxorGTP:Ct Ternary Complex, 50 mM Mg2+ (2160 min)
Components
  • DNA (5'-D(*CP*GP*GP*CP*CP*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
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: 1.56 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 6, 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*CP*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)45,90014
Polymers45,1544
Non-polymers74710
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5650 Å2
ΔGint-43 kcal/mol
Surface area16000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.200, 62.130, 118.533
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*CP*TP*AP*CP*G)-3')


Mass: 2716.787 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, 362 molecules

#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


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


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


Mass: 154.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O2S2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.45 Å3/Da / Density % sol: 49.89 % / Mosaicity: 0.137 °
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: Aug 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 63490 / % possible obs: 99 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.031 / Rrim(I) all: 0.083 / Χ2: 0.993 / Net I/σ(I): 10.8 / Num. measured all: 426304
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.56-1.595.90.91131480.7460.3990.9981.01199.7
1.59-1.626.60.79731310.7740.3310.8651.02799.9
1.62-1.656.80.68831840.8250.2810.7441.01399.7
1.65-1.686.80.56431480.8770.230.611.01699.7
1.68-1.726.70.47431830.9170.1950.5141.02399.8
1.72-1.766.60.40730850.9230.1690.4421.0698.8
1.76-1.86.20.33731580.9340.1460.3681.06998.7
1.8-1.856.10.25930540.9590.1130.2841.08696.8
1.85-1.97.20.2331610.9780.0910.2471.12399.1
1.9-1.977.20.18431590.9840.0720.1981.07799.4
1.97-2.047.20.1531570.9890.0590.1611.08899.5
2.04-2.1270.12431920.9910.050.1341.03699.2
2.12-2.216.90.10431670.9930.0420.1130.95699.8
2.21-2.336.70.08732090.9940.0360.0950.93799.5
2.33-2.486.50.07731440.9950.0320.0840.91198.2
2.48-2.6760.0731110.9950.030.0760.88897.2
2.67-2.947.40.06532370.9970.0250.070.9199.6
2.94-3.367.20.0632390.9970.0240.0650.92299.4
3.36-4.236.80.05532730.9970.0220.0590.91199.5
4.23-506.40.05633500.990.0240.0620.896.5

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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: 1.56→34.928 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1818 3155 4.97 %
Rwork0.165 60264 -
obs0.1658 63419 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 66.19 Å2 / Biso mean: 26.8957 Å2 / Biso min: 12.93 Å2
Refinement stepCycle: final / Resolution: 1.56→34.928 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2541 342 26 356 3265
Biso mean--40.77 35.8 -
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 (%)
1.56-1.58310.25651360.2405259498
1.5831-1.60780.2481340.22732599100
1.6078-1.63420.22011470.20182600100
1.6342-1.66230.19271250.19772615100
1.6623-1.69260.20451320.18252594100
1.6926-1.72510.18271430.17252614100
1.7251-1.76030.16871300.1719258999
1.7603-1.79860.2111380.169258499
1.7986-1.84040.18091580.1701250796
1.8404-1.88650.18651130.1702263299
1.8865-1.93750.24361270.1672260799
1.9375-1.99450.20051350.16142600100
1.9945-2.05880.17171300.1654263499
2.0588-2.13240.1721340.1677260199
2.1324-2.21780.16921550.15642655100
2.2178-2.31870.18361250.1484261099
2.3187-2.44090.14931420.1493261599
2.4409-2.59380.18881350.1547256397
2.5938-2.7940.19811390.1617264699
2.794-3.0750.17481500.17282661100
3.075-3.51960.16661440.15892673100
3.5196-4.43290.15761340.1473272299
4.4329-34.9280.20381490.1812274996
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)
11.1023-0.1285-0.28061.05570.31061.0430.01960.0158-0.04220.057-0.0413-0.0488-0.04460.0755-0.00240.13310.0031-0.02350.1524-0.00340.13065.0467-4.5641-11.8392
20.10420.088-0.09690.0946-0.12430.17880.1540.1203-0.0261-0.5858-0.15680.1264-0.2779-0.16860.00250.26820.0374-0.03170.2048-0.03840.1672-2.2643-6.4321-25.7362
30.02280.0001-0.00080.01360.01230.01110.10980.0185-0.1086-0.011-0.08870.06230.07490.0349-00.2396-0.018-0.02440.22190.0050.16873.28214.1224-18.8551
40.4446-0.51850.67320.6111-0.79251.02740.0142-0.1129-0.1433-0.16820.19720.00590.2084-0.23230.0790.20170.0089-0.01040.2323-0.05280.186.5602-20.0615-29.4646
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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