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- PDB-6wic: Pre-catalytic quaternary complex of human Polymerase Mu on a comp... -

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Basic information

Entry
Database: PDB / ID: 6wic
TitlePre-catalytic quaternary complex of human Polymerase Mu on a complementary DNA double-strand break substrate
Components
  • DNA (5'-D(*AP*CP*G)-3')
  • DNA (5'-D(*CP*GP*GP*CP*AP*T)-3')
  • DNA (5'-D(*CP*GP*TP*A)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA-directed DNA/RNA polymerase mu
KeywordsTRANSFERASE/DNA / Family X polymerase / nonhomologous end-joining / DNA double-strand break repair / TRANSFERASE-DNA complex
Function / homology
Function and homology information


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 / nucleus / metal ion binding
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'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE / : / DI(HYDROXYETHYL)ETHER / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsKaminski, A.M. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIA ES 102645 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065070 United States
CitationJournal: Nat Commun / Year: 2020
Title: Structural snapshots of human DNA polymerase mu engaged on a DNA double-strand break.
Authors: Kaminski, A.M. / Pryor, J.M. / Ramsden, D.A. / Kunkel, T.A. / Pedersen, L.C. / Bebenek, K.
History
DepositionApr 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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*T)-3')
U: DNA (5'-D(*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)46,18314
Polymers45,1335
Non-polymers1,0509
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6710 Å2
ΔGint-49 kcal/mol
Surface area15800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.134, 62.233, 118.054
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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 / Fragment: UNP residues 132-494 / Mutation: P398-P410 deletion replaced by G410 linker
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): Rosetta2 (DE3) / References: UniProt: Q9NP87, DNA-directed DNA polymerase

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DNA chain , 4 types, 4 molecules TUPD

#2: DNA chain DNA (5'-D(*CP*GP*GP*CP*AP*T)-3')


Mass: 1809.217 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*CP*G)-3')


Mass: 886.637 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: 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)
#5: 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 , 9 types, 358 molecules

#6: Chemical ChemComp-DUP / 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#12: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#13: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 40-45.5 mM MES, pH 5.6, 0.16-0.182 M potassium chloride, 8.2-9.1 mM magnesium sulfate, 8.2-9.1% w/v PEG400

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 5, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 64813 / % possible obs: 99.5 % / Redundancy: 6.4 % / Biso Wilson estimate: 18.58 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rpim(I) all: 0.027 / Rrim(I) all: 0.067 / Rsym value: 0.062 / Χ2: 0.596 / Net I/σ(I): 26.6
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3163 / CC1/2: 0.778 / CC star: 0.936 / Rpim(I) all: 0.275 / Rrim(I) all: 0.604 / Rsym value: 0.535 / Χ2: 0.311 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4M04

4m04


Resolution: 1.55→34.88 Å / SU ML: 0.1514 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.4529
RfactorNum. reflection% reflectionSelection details
Rfree0.1794 1995 3.08 %random
Rwork0.1655 ---
obs0.166 64729 99.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24.42 Å2
Refinement stepCycle: LAST / Resolution: 1.55→34.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2563 341 59 349 3312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00893237
X-RAY DIFFRACTIONf_angle_d1.03774480
X-RAY DIFFRACTIONf_chiral_restr0.0603488
X-RAY DIFFRACTIONf_plane_restr0.0072520
X-RAY DIFFRACTIONf_dihedral_angle_d12.74521021
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.25741370.21814350X-RAY DIFFRACTION97.63
1.59-1.630.18611420.18624424X-RAY DIFFRACTION99.54
1.63-1.680.22481400.18244427X-RAY DIFFRACTION99.72
1.68-1.730.18761420.16814450X-RAY DIFFRACTION99.76
1.73-1.80.2211480.16074431X-RAY DIFFRACTION99.89
1.8-1.870.18531340.15784450X-RAY DIFFRACTION99.8
1.87-1.950.1751450.15954460X-RAY DIFFRACTION99.37
1.95-2.060.17811470.15984463X-RAY DIFFRACTION99.78
2.06-2.180.18991390.16684482X-RAY DIFFRACTION99.85
2.18-2.350.17031430.15754492X-RAY DIFFRACTION99.91
2.35-2.590.18091440.16524516X-RAY DIFFRACTION99.96
2.59-2.960.20681430.17394529X-RAY DIFFRACTION99.36
2.96-3.730.17411420.16584553X-RAY DIFFRACTION99.24
3.73-34.880.15241490.15994707X-RAY DIFFRACTION98.36
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)
10.9380313585970.0634616996039-0.3747488598630.9833859528530.06008095980970.48339911105-0.0473604223243-0.00309928844968-0.1866023221630.0378442257068-0.0343336505864-0.2057125320340.06798022365850.112449904167-0.04992445983630.1557211890620.034318990352-0.02900869270940.168534078899-0.00749667435270.24371341670415.4219308218-18.1861708058-17.9681173602
20.00842234080879-0.2085397464590.05752408595160.4472891036270.3536016322520.2390911450150.0491851932525-0.04858293197970.120983068412-0.096812940565-0.00172231338213-0.207650580207-0.192009338810.195069375272-1.1482577023E-90.198658229672-0.02894407157590.01913719261470.208500151886-0.005117254757020.21318749766616.83642163219.37240725014-18.9437286415
30.7691378866570.122326191295-0.04790411128670.7527682715580.07922636232580.3930178676140.0380834175321-0.1235806240570.09367110844520.192884180534-0.0181190804182-0.00781121717515-0.08522658237428.49844725779E-5-0.004173357987660.185507977659-0.005501968189310.00388509243990.163787551918-0.03117355746060.130285359118-0.6054476355596.71722707241-1.11153637082
40.743106587891-0.530877687509-0.1579961289610.9705852437740.224425339651.022732163870.01554845077390.0578623692081-0.2327846926250.0469147620672-0.10267058920.1506677626930.00646518407314-0.0601375494956-0.05997558959840.1307761701830.0001204211369980.00129947713070.148304550391-0.03908713862070.17896595576-8.29128925529-12.3155351318-12.4471628564
5-0.02262069409510.200523438465-0.1752266899740.383629027651-0.04190040500520.182880976392-0.0207232308524-0.0219662611857-0.0767177705182-0.1939651680830.04995442701470.04461362915290.00614850167337-0.09518483899860.0007111926914860.1957036985780.0125717529811-0.0347964410550.190755681285-0.05120356458970.1629338607622.44967829987-15.2453886273-30.6640087754
60.06520016223430.0282000208453-0.02045527212430.1130545294460.08444173025840.1151543853210.05035028137410.0346954560123-0.08728842384280.0562737174111-0.0644479427233-0.01515434771970.01267393960810.0247364229609-1.24770616912E-60.1859969414750.0188291375646-0.002128694403950.1730842131860.0026096283490.134041427433-0.3499441630674.53577324964-18.6464885759
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 135:231
2X-RAY DIFFRACTION2chain A and resid 232:289
3X-RAY DIFFRACTION3chain A and resid 290:423
4X-RAY DIFFRACTION4chain A and resid 424:494
5X-RAY DIFFRACTION5chain T or chain D
6X-RAY DIFFRACTION6chain U or chain P

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