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- PDB-7ksz: DNA Polymerase Mu, dGTP:At Pre-Catalytic Ground State Ternary Com... -

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Basic information

Entry
Database: PDB / ID: 7ksz
TitleDNA Polymerase Mu, dGTP:At Pre-Catalytic Ground State Ternary Complex, 10 mM Ca2+ (960min)
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/DNA / time-lapse crystallography / oxidized nucleotide insertion / DNA polymerase mu / double strand break repair / REPLICATION / REPLICATION-DNA complex
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'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / 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: 1.417 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 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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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)46,61517
Polymers45,1784
Non-polymers1,43713
Water7,782432
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-41 kcal/mol
Surface area16020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.753, 68.778, 110.133
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.) Homo sapiens (human)
#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.) 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, 445 molecules

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


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#8: 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
#9: 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
#10: Chemical ChemComp-DGT / 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.5 Å3/Da / Density % sol: 50.89 % / Mosaicity: 0.137 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 85-90mM HEPES pH 7.5, 17-18% PEG 4000

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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: Dec 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.417→50 Å / Num. obs: 86531 / % possible obs: 99.8 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.046 / Rrim(I) all: 0.108 / Χ2: 1.083 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.42-1.445.10.91942790.6480.441.0211.059100
1.44-1.475.50.76442870.7540.3540.8431.063100
1.47-1.55.60.64442580.8180.2940.7091.0999.8
1.5-1.535.60.51342890.8780.2340.5651.09499.7
1.53-1.565.50.43242520.90.1990.4771.199.9
1.56-1.65.40.35942780.9220.1670.3971.13399.9
1.6-1.645.20.28542730.9480.1360.3161.15999.8
1.64-1.684.80.23342960.9560.1170.2621.15699.7
1.68-1.735.40.20443000.9730.0960.2251.137100
1.73-1.795.80.18143170.9750.0820.1991.135100
1.79-1.855.80.15742850.9810.0710.1731.134100
1.85-1.935.70.13443210.9830.0610.1471.13100
1.93-2.015.60.11943040.9850.0550.1321.086100
2.01-2.125.50.10643460.9860.050.1171.087100
2.12-2.255.20.09542960.9870.0460.1061.07899.6
2.25-2.434.80.08443560.9870.0420.0941.03999.8
2.43-2.6760.08743690.9880.0390.0951.006100
2.67-3.065.90.08544090.9890.0380.0940.986100
3.06-3.855.60.08244290.9880.0390.091199.9
3.85-505.10.08145870.9860.040.091198.8

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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: 1.417→32.826 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1747 4328 5.01 %
Rwork0.1573 82125 -
obs0.1582 86453 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.15 Å2 / Biso mean: 21.6426 Å2 / Biso min: 7.68 Å2
Refinement stepCycle: final / Resolution: 1.417→32.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2533 344 63 444 3384
Biso mean--31.69 32.87 -
Num. residues----342
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013261
X-RAY DIFFRACTIONf_angle_d1.1974525
X-RAY DIFFRACTIONf_dihedral_angle_d17.3711231
X-RAY DIFFRACTIONf_chiral_restr0.08492
X-RAY DIFFRACTIONf_plane_restr0.009528
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4173-1.43340.311340.2845255393
1.4334-1.45030.27441410.23862685100
1.4503-1.4680.24461460.22382743100
1.468-1.48650.23431420.2142699100
1.4865-1.50610.23781420.20352697100
1.5061-1.52670.23811430.19262725100
1.5267-1.54850.21891430.19172727100
1.5485-1.57170.21061440.17472719100
1.5717-1.59620.20581420.17212689100
1.5962-1.62240.18761440.16392737100
1.6224-1.65040.18631420.15892692100
1.6504-1.68040.16521430.14822732100
1.6804-1.71270.1811440.15322723100
1.7127-1.74760.16061430.14972721100
1.7476-1.78560.18871440.15052738100
1.7856-1.82720.16711440.14892724100
1.8272-1.87290.15861430.14922726100
1.8729-1.92350.15971420.15052747100
1.9235-1.98010.18241420.15262741100
1.9801-2.0440.18531490.1522732100
2.044-2.1170.15751470.14992754100
2.117-2.20180.16881420.14292744100
2.2018-2.3020.15151480.1395273699
2.302-2.42330.15181430.13992746100
2.4233-2.57510.16551440.14392754100
2.5751-2.77380.16411490.15262795100
2.7738-3.05270.16531460.15622790100
3.0527-3.4940.1651470.14652804100
3.494-4.40050.13761480.1443280799
4.4005-32.8260.21941570.1846294599
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)
10.7292-0.14470.20430.7559-0.13350.9522-0.00170.1355-0.1332-0.1036-0.0443-0.08610.15880.177200.15240.0365-0.00120.1477-0.02260.137212.1423-18.8786-14.3572
20.32250.0130.08020.30650.34180.55880.05260.11910.1359-0.1994-0.0001-0.2936-0.17670.14460.00010.1735-0.01050.04990.19110.02430.209817.91387.1341-17.4724
31.2052-0.0401-0.1481.40510.12090.61240.02860.02570.08530.0424-0.0118-0.0015-0.021-0.02980.00260.07010.00270.00310.07820.00820.0648-5.49820.8477-4.9824
40.14480.12110.05890.10120.04920.0240.06180.2884-0.0707-0.6464-0.1085-0.06970.0247-0.27710.00240.29780.036-0.00580.26-0.0540.1322-0.3828-15.3189-31.1424
50.0084-0.0165-0.01170.21080.05580.02230.08070.15180.035-0.0859-0.09020.1289-0.0321-0.0222-0.0030.17450.0023-0.01370.20290.01430.1236-5.04811.1254-18.6964
60.03770.00380.01830.03950.03050.02990.1704-0.1121-0.05150.1402-0.01790.12840.26330.005800.1947-0.0217-0.00320.18260.02370.11733.15555.4359-17.9192
70.0820.0235-0.02250.4996-0.35440.25180.03080.1155-0.0423-0.18890.00390.03170.2352-0.16660.14390.21830.0033-0.02030.2519-0.08260.11443.2205-21.8199-25.7917
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 138 through 228)A138 - 228
2X-RAY DIFFRACTION2(chain 'A' and resid 229 through 287)A229 - 287
3X-RAY DIFFRACTION3(chain 'A' and resid 288 through 494)A288 - 494
4X-RAY DIFFRACTION4(chain 'T' and resid 1 through 4)T1 - 4
5X-RAY DIFFRACTION5(chain 'T' and resid 5 through 9)T5 - 9
6X-RAY DIFFRACTION6(chain 'P' and resid 1 through 4)P1 - 4
7X-RAY DIFFRACTION7(chain 'D' and resid 1 through 4)D1 - 4

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