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- PDB-4qz8: Mouse Tdt in complex with a DSB substrate, C-G base pair -

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Basic information

Entry
Database: PDB / ID: 4qz8
TitleMouse Tdt in complex with a DSB substrate, C-G base pair
Components
  • 5'-D(*AP*AP*AP*AP*AP*C)-3'
  • 5'-D(*TP*TP*TP*TP*TP*GP*G)-3'
  • DNA nucleotidylexotransferaseTerminal deoxynucleotidyl transferase
KeywordsTRANSFERASE/DNA / Terminal deoxynucleotidyltransferase / nucleus / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase activity ...DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / DNA modification / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / DNA metabolic process / response to ATP / euchromatin / nuclear matrix / double-strand break repair via nonhomologous end joining / DNA-directed DNA polymerase activity / hydrolase activity / chromatin / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
DNA nucleotidylexotransferase (TdT) / 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 / breast cancer carboxy-terminal domain / DNA polymerase lambda, fingers domain ...DNA nucleotidylexotransferase (TdT) / 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 / 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
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGouge, J. / Delarue, M.
CitationJournal: Embo J. / Year: 2015
Title: Structural basis for a novel mechanism of DNA bridging and alignment in eukaryotic DSB DNA repair.
Authors: Gouge, J. / Rosario, S. / Romain, F. / Poitevin, F. / Beguin, P. / Delarue, M.
History
DepositionJul 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.2Sep 20, 2023Group: 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 / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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
D: 5'-D(*AP*AP*AP*AP*AP*C)-3'
T: 5'-D(*TP*TP*TP*TP*TP*GP*G)-3'
U: 5'-D(*AP*AP*AP*AP*AP*C)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9577
Polymers51,4594
Non-polymers4983
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-35 kcal/mol
Surface area18330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.329, 74.259, 118.969
Angle α, β, γ (deg.)90.00, 97.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein DNA nucleotidylexotransferase / Terminal deoxynucleotidyl transferase / Terminal addition enzyme / Terminal deoxynucleotidyltransferase / TDT / Terminal transferase


Mass: 45704.008 Da / Num. of mol.: 1 / Fragment: SEE REMARK 999
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dntt, Tdt / Production host: Escherichia coli (E. coli) / References: UniProt: P09838, DNA nucleotidylexotransferase

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DNA chain , 2 types, 3 molecules DUT

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


Mass: 1810.258 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: DNA chain 5'-D(*TP*TP*TP*TP*TP*GP*G)-3'


Mass: 2134.418 Da / Num. of mol.: 1 / Source method: obtained synthetically

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Non-polymers , 4 types, 92 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#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.: 89 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPROTEIN COMPRISES UNP RESIDUES 132-482 AND 503-530 WITH 483-502 DELETED.

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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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 12-17% PEG4000, 9-12% isopropanol, 100 mM sodium acetate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 30, 2012
Details: Pt-coated mirrors in a Kirkpatrick-Baez (KB) geometry
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.7→41.7 Å / Num. obs: 14082 / % possible obs: 99.3 % / Redundancy: 4.1 % / Biso Wilson estimate: 91.68 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2042 / % possible all: 99.8

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Processing

Software
NameVersionClassification
DNAdata collection
PHASERphasing
BUSTER2.10.1refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4I2A

4i2a


Resolution: 2.7→31.41 Å / Cor.coef. Fo:Fc: 0.9248 / Cor.coef. Fo:Fc free: 0.9126 / SU R Cruickshank DPI: 0.798 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.801 / SU Rfree Blow DPI: 0.298 / SU Rfree Cruickshank DPI: 0.301 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 705 5.01 %RANDOM
Rwork0.2037 ---
obs0.2054 14080 99.33 %-
Displacement parametersBiso mean: 88.12 Å2
Baniso -1Baniso -2Baniso -3
1--5.9614 Å20 Å220.8161 Å2
2--2.0457 Å20 Å2
3---3.9156 Å2
Refine analyzeLuzzati coordinate error obs: 0.49 Å
Refinement stepCycle: LAST / Resolution: 2.7→31.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2642 367 29 89 3127
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013159HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.974362HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1322SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes425HARMONIC5
X-RAY DIFFRACTIONt_it3159HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion2.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion417SEMIHARMONIC5
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_contact3369SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.92 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.3472 142 4.92 %
Rwork0.2442 2743 -
all0.2491 2885 -
obs--99.33 %
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)
13.4325-2.94950.18415.97390.07592.38120.1073-0.30130.3885-0.2298-0.00320.51740.1221-0.5918-0.1041-0.09120.1668-0.00390.034-0.0948-0.0824-4.62797.968119.2064
26.26350.8825-0.96271.45830.01772.96530.3328-0.5498-0.44730.5579-0.259-0.05970.15870.0018-0.07380.0020.0021-0.1114-0.0776-0.1532-0.3246-2.0534-1.215441.5905
36.75461.81212.91863.8499-2.68485.53580.2282-0.6106-0.37050.3352-0.3313-0.16340.13360.43570.1031-0.2006-0.0884-0.13750.3040.108-0.344510.6218-4.04849.5748
43.1017-0.9678-0.08222.3984-0.37653.53710.3129-0.51240.3781-0.0924-0.1814-0.56250.04750.451-0.1315-0.08380.1682-0.1088-0.0279-0.105-0.014116.53520.010726.0307
50.9513-2.57541.07765.9048-2.59277.6332-0.15540.0749-0.3236-0.44570.4198-0.4320.5639-0.2815-0.26440.20950.1585-0.1105-0.1072-0.0358-0.12362.7465-9.4414.7172
61.1065-2.66053.06550.40420.17010.8377-0.08960.0176-0.1367-0.0833-0.1649-0.05690.22670.02330.25460.03990.022-0.1786-0.2897-0.13010.25910.7927-15.715736.9977
72.63772.66942.27365.28921.92247.9068-0.00960.06260.02650.05420.1313-0.2460.11880.0852-0.12170.11160.1532-0.11990.04140.0016-0.1556-0.2995-3.44078.4159
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|148 - 227}A148 - 227
2X-RAY DIFFRACTION2{A|228 - 354}A228 - 354
3X-RAY DIFFRACTION3{A|355 - 429}A355 - 429
4X-RAY DIFFRACTION4{A|430 - 510}A430 - 510
5X-RAY DIFFRACTION5{T|1 - 7}T1 - 7
6X-RAY DIFFRACTION6{U|1 - 6}U1 - 6
7X-RAY DIFFRACTION7{D|1 - 6}D1 - 6

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