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- PDB-6go6: TdT chimera (Loop1 of pol mu) - ternary complex with downstream dsDNA -

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Basic information

Entry
Database: PDB / ID: 6go6
TitleTdT chimera (Loop1 of pol mu) - ternary complex with downstream dsDNA
Components
  • DNA (5'-D(*AP*AP*AP*AP*AP*C)-3')
  • DNA (5'-D(*TP*TP*TP*TP*TP*GP*GP*C)-3')
  • DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase
KeywordsDNA BINDING PROTEIN / NHEJ pathway / DNA bridging / DNA polymerase polX
Function / homology
Function and homology information


DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / Nonhomologous End-Joining (NHEJ) / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / somatic hypermutation of immunoglobulin genes / B cell differentiation / euchromatin ...DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / Nonhomologous End-Joining (NHEJ) / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / somatic hypermutation of immunoglobulin genes / B cell differentiation / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / hydrolase activity / chromatin / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain ...DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Polymerase, nucleotidyl transferase domain / Nucleotidyltransferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / BRCA1 C Terminus (BRCT) domain / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / breast cancer carboxy-terminal domain / 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 lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE / DNA / DNA nucleotidylexotransferase / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsLoc'h, J. / Gerodimos, C.A. / Rosario, S. / Lieber, M.R. / Delarue, M.
Funding support France, 1items
OrganizationGrant numberCountry
Fondation ARC pour la recherche sur le cancer France
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Structural evidence for an intransbase selection mechanism involving Loop1 in polymerase mu at an NHEJ double-strand break junction.
Authors: Loc'h, J. / Gerodimos, C.A. / Rosario, S. / Tekpinar, M. / Lieber, M.R. / Delarue, M.
History
DepositionJun 1, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase
G: DNA (5'-D(*TP*TP*TP*TP*TP*GP*GP*C)-3')
F: DNA (5'-D(*TP*TP*TP*TP*TP*GP*GP*C)-3')
E: DNA (5'-D(*AP*AP*AP*AP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,0057
Polymers52,5064
Non-polymers4983
Water5,927329
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-42 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.420, 189.830, 46.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase / Terminal addition enzyme / Terminal deoxynucleotidyltransferase / Terminal transferase / Pol Mu / ...Terminal addition enzyme / Terminal deoxynucleotidyltransferase / Terminal transferase / Pol Mu / Terminal transferase / Terminal addition enzyme / Terminal deoxynucleotidyltransferase / Terminal transferase


Mass: 45848.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.,There is an insertion of one residue between loop1 of pol ...Details: There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.,There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.,There is an insertion of one residue between loop1 of pol mu and TdT (Q394). This insertion explain the numbering shift with wt-TdT.
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dntt, Tdt, Polm, polmu / Production host: Escherichia coli (E. coli)
References: UniProt: P09838, UniProt: Q9JIW4, DNA nucleotidylexotransferase, DNA-directed DNA polymerase

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DNA chain , 2 types, 3 molecules GFE

#2: DNA chain DNA (5'-D(*TP*TP*TP*TP*TP*GP*GP*C)-3')


Mass: 2423.600 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*AP*AP*AP*C)-3')


Mass: 1810.258 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 332 molecules

#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-DCT / 2',3'-DIDEOXYCYTIDINE 5'-TRIPHOSPHATE


Type: DNA linking / Mass: 451.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O12P3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / Source method: isolated from a natural source / Formula: H2O

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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: 3.63 Å3/Da / Density % sol: 66.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 19-25% PEG 4000, 100-400 mM lithium sulfate, 100 mM tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.09→47.46 Å / Num. obs: 45742 / % possible obs: 98.9 % / Redundancy: 5.4 % / Biso Wilson estimate: 58.43 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 15.79
Reflection shellResolution: 2.09→2.22 Å / Rmerge(I) obs: 1.07 / Num. unique obs: 6958 / CC1/2: 0.612 / % possible all: 94.1

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JMS

1jms


Resolution: 2.09→47.46 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.897 / SU R Cruickshank DPI: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.155 / SU Rfree Blow DPI: 0.143 / SU Rfree Cruickshank DPI: 0.137
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2288 5 %RANDOM
Rwork0.202 ---
obs0.204 45742 98.7 %-
Displacement parametersBiso mean: 61.89 Å2
Baniso -1Baniso -2Baniso -3
1-11.8782 Å20 Å20 Å2
2---14.44 Å20 Å2
3---2.5618 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: 1 / Resolution: 2.09→47.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 424 29 329 3654
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013439HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.974728HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1163SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes462HARMONIC5
X-RAY DIFFRACTIONt_it3439HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.7
X-RAY DIFFRACTIONt_other_torsion17.21
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion437SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3575SEMIHARMONIC4
LS refinement shellResolution: 2.09→2.14 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2789 142 5 %
Rwork0.2806 2697 -
all0.2805 2839 -
obs--84.48 %
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)
10.97690.4044-0.11670.78590.1151.1398-0.0725-0.01760.0879-0.11230.02480.02940.0454-0.0530.04770.0095-0.00720.0039-0.10930.047-0.1668-7.515338.6958-8.0063
23.39972.1977-0.80451.38120.65447.2051-0.04720.5311-0.2001-0.1636-0.0066-0.49930.53230.27670.05380.23360.06680.0923-0.27720.0117-0.29630.012118.9098-16.5525
36.0242-1.4593-2.85427.7408-2.91045.75880.0587-0.0089-0.5372-0.2434-0.10430.33150.2157-0.40310.04560.28510.0296-0.0381-0.3040.0033-0.2361-0.800812.878-8.1746
44.9532-2.9104-1.11358.1301-2.88918.31540.0166-0.4012-0.5009-0.2455-0.13940.4060.41940.02110.12270.3040.152-0.1127-0.2994-0.04690.22530.27946.8577-6.8643
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ C|* }
3X-RAY DIFFRACTION3{ D|* }
4X-RAY DIFFRACTION4{ F|* }

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