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- PDB-4htp: Crystal structure of the DBD domain of human DNA ligase IV bound ... -

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Basic information

Entry
Database: PDB / ID: 4htp
TitleCrystal structure of the DBD domain of human DNA ligase IV bound to Artemis peptide
Components
  • DNA ligase 4
  • Protein artemis
KeywordsLIGASE/HYDROLASE / Helical domain / DNA binding domain / DNA / artemis / LIGASE-HYDROLASE complex
Function / homology
Function and homology information


DNA ligation involved in DNA recombination / positive regulation of chromosome organization / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase activity / DN2 thymocyte differentiation / DNA ligase (ATP) / T cell receptor V(D)J recombination / pro-B cell differentiation / DNA ligase (ATP) activity ...DNA ligation involved in DNA recombination / positive regulation of chromosome organization / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase activity / DN2 thymocyte differentiation / DNA ligase (ATP) / T cell receptor V(D)J recombination / pro-B cell differentiation / DNA ligase (ATP) activity / single-stranded DNA endodeoxyribonuclease activity / DNA-dependent protein kinase-DNA ligase 4 complex / single strand break repair / immunoglobulin V(D)J recombination / nonhomologous end joining complex / 5'-3' exonuclease activity / DNA ligation / V(D)J recombination / double-strand break repair via classical nonhomologous end joining / isotype switching / nucleotide-excision repair, DNA gap filling / positive regulation of neurogenesis / 5'-3' DNA exonuclease activity / response to ionizing radiation / DNA biosynthetic process / cellular response to lithium ion / 2-LTR circle formation / somatic stem cell population maintenance / ligase activity / response to X-ray / chromosome organization / interstrand cross-link repair / condensed chromosome / telomere maintenance / neurogenesis / B cell differentiation / central nervous system development / stem cell proliferation / cellular response to ionizing radiation / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / establishment of integrated proviral latency / double-strand break repair / positive regulation of fibroblast proliferation / T cell differentiation in thymus / fibroblast proliferation / endonuclease activity / neuron apoptotic process / in utero embryonic development / adaptive immune response / negative regulation of neuron apoptotic process / cell population proliferation / damaged DNA binding / chromosome, telomeric region / Hydrolases; Acting on ester bonds / cell cycle / cell division / intracellular membrane-bounded organelle / Golgi apparatus / magnesium ion binding / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus ...DNA ligase i, domain 1 / DNA ligase, ATP-dependent, N-terminal domain / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / ATP-dependent DNA ligase signature 2. / ATP-dependent DNA ligase AMP-binding site. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / DNA repair metallo-beta-lactamase / DNA repair metallo-beta-lactamase / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Nucleic acid-binding, OB-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA ligase 4 / Protein artemis
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2502 Å
AuthorsDe Ioannes, P.E. / Aggarwal, A.K.
CitationJournal: Cell Rep / Year: 2012
Title: Structural Basis of DNA Ligase IV-Artemis Interaction in Nonhomologous End-Joining.
Authors: De Ioannes, P. / Malu, S. / Cortes, P. / Aggarwal, A.K.
History
DepositionNov 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Sep 20, 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

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Assembly

Deposited unit
A: DNA ligase 4
B: DNA ligase 4
C: Protein artemis
E: Protein artemis


Theoretical massNumber of molelcules
Total (without water)57,5974
Polymers57,5974
Non-polymers00
Water4,125229
1
A: DNA ligase 4
C: Protein artemis


Theoretical massNumber of molelcules
Total (without water)28,7982
Polymers28,7982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-9 kcal/mol
Surface area11350 Å2
MethodPISA
2
B: DNA ligase 4
E: Protein artemis


Theoretical massNumber of molelcules
Total (without water)28,7982
Polymers28,7982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-6 kcal/mol
Surface area11530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.210, 72.830, 158.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA ligase 4 / / DNA ligase IV / Polydeoxyribonucleotide synthase [ATP] 4


Mass: 27345.660 Da / Num. of mol.: 2 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CP RIPL / References: UniProt: P49917, DNA ligase (ATP)
#2: Protein/peptide Protein artemis / DNA cross-link repair 1C protein / Protein A-SCID / SNM1 homolog C / hSNM1C / SNM1-like protein


Mass: 1452.653 Da / Num. of mol.: 2 / Fragment: C-terminal / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human)
References: UniProt: Q96SD1, Hydrolases; Acting on ester bonds
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 3.06 Å3/Da / Density % sol: 59.78 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18% PEG 1000, 200 mM Tris-HCl pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9394 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 9, 2010 / Details: bending magnet
RadiationMonochromator: Toroidal focusing mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9394 Å / Relative weight: 1
ReflectionResolution: 2.25→40 Å / Num. all: 32066 / Num. obs: 24874 / % possible obs: 91.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 12.4 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 31.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
2.25-2.337.60.6632.323990.15669.2
2.33-2.4290.563327300.1879.7
2.42-2.5310.40.4784.629320.24485.4
2.53-2.6711.70.3926.6331420.31891.2
2.67-2.8313.10.3319.833290.42496.3
2.83-3.0514.20.24117.134220.68396.6
3.05-3.3614.40.1629.134191.22298.9
3.36-3.85140.10450.934912.59899.1
3.85-4.8413.60.07671.335084.35599.3
4.84-4013.30.05585.136944.85499

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HTO

4hto


Resolution: 2.2502→33.073 Å / SU ML: 0.26 / σ(F): 1 / σ(I): 2 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2494 1421 5.13 %random
Rwork0.1962 ---
all0.1989 32066 --
obs0.1989 27703 80.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2502→33.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3643 0 0 229 3872
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083710
X-RAY DIFFRACTIONf_angle_d1.0675005
X-RAY DIFFRACTIONf_dihedral_angle_d16.0841378
X-RAY DIFFRACTIONf_chiral_restr0.067575
X-RAY DIFFRACTIONf_plane_restr0.004633
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2502-2.33060.3462580.2596878X-RAY DIFFRACTION28
2.3306-2.42380.2933960.24371522X-RAY DIFFRACTION48
2.4238-2.53410.2657880.23322027X-RAY DIFFRACTION63
2.5341-2.66770.27831370.23272515X-RAY DIFFRACTION78
2.6677-2.83470.3121830.24052973X-RAY DIFFRACTION93
2.8347-3.05340.28631730.23183198X-RAY DIFFRACTION98
3.0534-3.36050.29141820.21943189X-RAY DIFFRACTION99
3.3605-3.84610.23251670.17623260X-RAY DIFFRACTION99
3.8461-4.84320.18771600.14883288X-RAY DIFFRACTION99
4.8432-33.07610.211770.17773432X-RAY DIFFRACTION99

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