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- PDB-7coc: Ternary complex of DNA polymerase Mu (K438A/Q441A) with 1-nt gapp... -

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Basic information

Entry
Database: PDB / ID: 7coc
TitleTernary complex of DNA polymerase Mu (K438A/Q441A) with 1-nt gapped DNA (T:dGMPNPP)
Components
  • DNA (5'-D(*CP*GP*GP*CP*TP*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
KeywordsHYDROLASE/DNA / polymerase mu / misincorporation / gap filling / mutagenesis / HYDROLASE / HYDROLASE-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
: / Chem-XG4 / DNA / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGuo, M. / Zhao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670819 China
CitationJournal: Nat Commun / Year: 2021
Title: Mechanism of genome instability mediated by human DNA polymerase mu misincorporation.
Authors: Guo, M. / Wang, Y. / Tang, Y. / Chen, Z. / Hou, J. / Dai, J. / Wang, Y. / Wang, L. / Xu, H. / Tian, B. / Hua, Y. / Zhao, Y.
History
DepositionAug 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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*TP*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)59,3898
Polymers58,7954
Non-polymers5944
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-35 kcal/mol
Surface area16630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.960, 68.560, 110.540
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: 53681.012 Da / Num. of mol.: 1 / Mutation: P410G, K438A, Q441A, deletion 398-409
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Plasmid: pET28a / 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*TP*TP*AP*CP*G)-3')


Mass: 2731.798 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 / Details: 5' phosphorylated dG / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 260 molecules

#5: Chemical ChemComp-XG4 / 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 1.93 Å3/Da / Density % sol: 36.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5 / Details: Hexylene glycol, HEPES, PEG10000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.899→29.132 Å / Num. obs: 36257 / % possible obs: 98.8 % / Redundancy: 5.459 % / Biso Wilson estimate: 30.02 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.063 / Χ2: 0.928 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.955.2990.6043.0513688266025830.8370.6797.1
1.95-25.3970.4423.8314080261126090.9030.48999.9
2-2.065.5980.3484.9314168253225310.9450.384100
2.06-2.125.5910.2776.3613738246524570.970.30599.7
2.12-2.195.6520.2037.8813452238423800.9860.22399.8
2.19-2.275.4020.1988.6212511233423160.9780.21999.2
2.27-2.365.450.14110.5912018222622050.990.15699.1
2.36-2.455.7140.1212.6512343216321600.9940.13299.9
2.45-2.565.610.10514.411567206720620.9950.11699.8
2.56-2.695.4760.0916.410793198319710.9950.09999.4
2.69-2.835.3040.07219.0910019190218890.9960.07999.3
2.83-35.6390.06122.8810089180717890.9970.06799
3-3.215.5620.05126.879267167916660.9980.05699.2
3.21-3.475.1560.04431.178007158615530.9980.04997.9
3.47-3.85.4190.0434.487733146914270.9980.04497.1
3.8-4.255.4170.03837.337026132812970.9980.04297.7
4.25-4.95.1710.03537.225988118611580.9980.03997.6
4.9-6.015.5010.03537.46542410249860.9980.03896.3
6.01-8.495.0440.03136.7939198047770.9990.03496.6
8.49-29.1324.7570.02639.2620984774410.9980.02992.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M04

4m04


Resolution: 1.9→29.132 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2115 1801 4.97 %
Rwork0.1816 34433 -
obs0.1831 36234 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.75 Å2 / Biso mean: 33.5882 Å2 / Biso min: 16.02 Å2
Refinement stepCycle: final / Resolution: 1.9→29.132 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2600 343 34 256 3233
Biso mean--34.42 39.51 -
Num. residues----344
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.95060.32651370.2798253397
1.9506-2.0080.25031320.2252663100
2.008-2.07280.23841400.21442637100
2.0728-2.14690.27891410.19972619100
2.1469-2.23280.24371560.19632633100
2.2328-2.33440.22351110.206264099
2.3344-2.45740.22041420.19012676100
2.4574-2.61130.23291420.20092627100
2.6113-2.81270.24591550.2014264199
2.8127-3.09550.21541300.2076267999
3.0955-3.54280.21821370.1785264698
3.5428-4.46090.16661350.1506266698
4.4609-29.1320.18211430.1546277397
Refinement TLS params.Method: refined / Origin x: 3.3254 Å / Origin y: 3.651 Å / Origin z: 11.767 Å
111213212223313233
T0.1708 Å2-0.0029 Å20.0001 Å2-0.1731 Å2-0.0038 Å2--0.1652 Å2
L0.3863 °20.0454 °20.0556 °2-0.2734 °2-0.0441 °2--0.3411 °2
S0.044 Å °-0.0487 Å °-0.0171 Å °0.0213 Å °-0.0358 Å °-0.0061 Å °-0.0047 Å °-0.0084 Å °-0 Å °
Refinement TLS groupSelection details: Chain A or Chain T or Chain P or Chain D

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