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- PDB-6go5: TdT chimera (Loop1 of pol mu) - Ternary complex with 1-nt gapped ... -

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Basic information

Entry
Database: PDB / ID: 6go5
TitleTdT chimera (Loop1 of pol mu) - Ternary complex with 1-nt gapped DNA substrate
Components
  • DNA (5'-D(*AP*CP*AP*GP*CP*G)-3')
  • DNA (5'-D(*CP*GP*CP*TP*GP*GP*CP*AP*AP*AP*CP*A)-3')
  • DNA (5'-D(*TP*GP*TP*TP*TP*G)-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
Chem-XC5 / DNA / DNA (> 10) / DNA nucleotidylexotransferase / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.35 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 1.1Aug 14, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_Rmerge_I_obs
Revision 1.2Dec 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

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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
B: DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase
H: DNA (5'-D(*CP*GP*CP*TP*GP*GP*CP*AP*AP*AP*CP*A)-3')
F: DNA (5'-D(*TP*GP*TP*TP*TP*G)-3')
G: DNA (5'-D(*AP*CP*AP*GP*CP*G)-3')
L: DNA (5'-D(*TP*GP*TP*TP*TP*G)-3')
N: DNA (5'-D(*CP*GP*CP*TP*GP*GP*CP*AP*AP*AP*CP*A)-3')
M: DNA (5'-D(*AP*CP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,33314
Polymers106,3088
Non-polymers1,0256
Water5,891327
1
A: DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase
H: DNA (5'-D(*CP*GP*CP*TP*GP*GP*CP*AP*AP*AP*CP*A)-3')
F: DNA (5'-D(*TP*GP*TP*TP*TP*G)-3')
G: DNA (5'-D(*AP*CP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6667
Polymers53,1544
Non-polymers5123
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-39 kcal/mol
Surface area18240 Å2
MethodPISA
2
B: DNA nucleotidylexotransferase,DNA-directed DNA/RNA polymerase mu,DNA nucleotidylexotransferase
L: DNA (5'-D(*TP*GP*TP*TP*TP*G)-3')
N: DNA (5'-D(*CP*GP*CP*TP*GP*GP*CP*AP*AP*AP*CP*A)-3')
M: DNA (5'-D(*AP*CP*AP*GP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6667
Polymers53,1544
Non-polymers5123
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-39 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)234.180, 69.250, 59.690
Angle α, β, γ (deg.)90.00, 95.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#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.: 2
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 , 3 types, 6 molecules HNFLGM

#2: DNA chain DNA (5'-D(*CP*GP*CP*TP*GP*GP*CP*AP*AP*AP*CP*A)-3')


Mass: 3656.407 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*GP*TP*TP*TP*G)-3')


Mass: 1830.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*AP*CP*AP*GP*CP*G)-3')


Mass: 1818.231 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 333 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-XC5 / 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidine


Mass: 465.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18N3O12P3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 2.27 Å3/Da / Density % sol: 45.74 %
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: ID29 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.35→44.86 Å / Num. obs: 39224 / % possible obs: 98.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 82.33 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.065 / Net I/σ(I): 10.54
Reflection shellResolution: 2.35→2.49 Å / Rmerge(I) obs: 0.813 / Num. unique obs: 6269 / CC1/2: 0.575 / % possible all: 98

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 2.35→44.86 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.363 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.376 / SU Rfree Blow DPI: 0.255 / SU Rfree Cruickshank DPI: 0.254
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1961 5 %RANDOM
Rwork0.218 ---
obs0.221 39208 98.3 %-
Displacement parametersBiso mean: 72.16 Å2
Baniso -1Baniso -2Baniso -3
1-2.1691 Å20 Å2-4.9936 Å2
2---0.7154 Å20 Å2
3----1.4537 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: 1 / Resolution: 2.35→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5215 936 60 327 6538
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.016429HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.058890HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2064SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes113HARMONIC2
X-RAY DIFFRACTIONt_gen_planes864HARMONIC5
X-RAY DIFFRACTIONt_it6429HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.62
X-RAY DIFFRACTIONt_other_torsion19.35
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion833SEMIHARMONIC5
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_contact6983SEMIHARMONIC4
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3257 144 5.02 %
Rwork0.2369 2724 -
all0.2414 2868 -
obs--97.75 %
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)
13.0632-0.8374-0.34791.33510.30221.2946-0.1942-0.5745-0.3030.1392-0.03130.0844-0.00150.30730.2255-0.17120.02030.0908-0.13970.1313-0.1287259.3763-6.914785.5462
21.1074-0.05060.17381.64280.07091.08490.01660.08150.13080.1396-0.15330.0465-0.03060.08350.1367-0.07490.02180.1031-0.15930.0281-0.0899261.518-39.990460.2082
30.5988-1.5017-3.32570.6008-1.67415.18190.0553-0.2596-0.0860.0891-0.01870.02960.29950.1142-0.03670.27270.0770.1652-0.29350.13820.1395262.9021-54.910464.3581
46.24291.19520.98337.8406-2.77825.39130.00010.032-0.3227-0.4953-0.32360.40620.5125-0.50070.32350.07920.07660.1098-0.2998-0.09620.0255252.3195-53.493259.3503
52.9811-0.2418-1.22826.52690.5222-0.24820.02060.1918-0.0454-0.02980.08660.1593-0.1644-0.1478-0.1073-0.3082-0.10570.0997-0.0067-0.07760.2845236.5725-44.911361.6476
60.77692.7678-3.14710.5835-0.02934.76940.0477-0.21-0.3723-0.1112-0.02720.14830.24340.3251-0.02060.27040.11880.1548-0.29050.16340.2675259.8989-22.22687.8399
78.2541-1.5709-1.19577.9723-0.79445.9885-0.0419-0.1777-0.1363-0.4799-0.19260.1030.5012-0.53860.2344-0.2122-0.02890.1059-0.299-0.00950.3135249.1634-19.705985.3109
82.21651.4418-1.52367.88450.5410.18880.00720.1386-0.0981-0.02960.02560.1288-0.2043-0.1224-0.0328-0.3121-0.05680.06870.30170.14480.3131234.2306-10.640290.8669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ D|* }
4X-RAY DIFFRACTION4{ E|* }
5X-RAY DIFFRACTION5{ F|* }
6X-RAY DIFFRACTION6{ G|* }
7X-RAY DIFFRACTION7{ H|* }
8X-RAY DIFFRACTION8{ I|* }

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