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- PDB-4hto: Crystal structure of the DBD domain of human DNA ligase IV Apo form -

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Basic information

Entry
Database: PDB / ID: 4hto
TitleCrystal structure of the DBD domain of human DNA ligase IV Apo form
ComponentsDNA ligase 4
KeywordsLIGASE / DNA binding protein / Helical domain / DNA binding domain
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 / DNA-dependent protein kinase-DNA ligase 4 complex / single strand break repair / immunoglobulin V(D)J recombination / nonhomologous end joining complex / DNA ligation / V(D)J recombination / double-strand break repair via classical nonhomologous end joining / isotype switching / positive regulation of neurogenesis / nucleotide-excision repair, DNA gap filling / DNA biosynthetic process / cellular response to lithium ion / 2-LTR circle formation / ligase activity / somatic stem cell population maintenance / response to X-ray / chromosome organization / condensed chromosome / neurogenesis / stem cell proliferation / central nervous system development / 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 / positive regulation of fibroblast proliferation / double-strand break repair / fibroblast proliferation / T cell differentiation in thymus / neuron apoptotic process / in utero embryonic development / negative regulation of neuron apoptotic process / cell population proliferation / chromosome, telomeric region / cell cycle / cell division / intracellular membrane-bounded organelle / 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 / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding, OB-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / DNA ligase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8068 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 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 ligase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5363
Polymers27,3461
Non-polymers1902
Water41423
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)196.236, 196.236, 196.236
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number210
Space group name H-MF4132
DetailsMonomeric assembly confirmed through gel filtration experiments

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Components

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


Mass: 27345.660 Da / Num. of mol.: 1 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CP RIPL / References: UniProt: P49917, DNA ligase (ATP)
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.8857.27
22.8857.27
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
293.151vapor diffusion, hanging drop716 % PEG 3350, 200 mM (NH4)3PO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
293.152vapor diffusion, hanging drop716 % PEG 3350, 200 mM (NH4)3SO4, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2902
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.9795
SYNCHROTRONNSLS X6A20.9791, 0.9537, 0.9796
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDMar 9, 2010Undulator
ADSC QUANTUM 2702CCDMar 9, 2010Bending magnet
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Hohzu HLH8-24SINGLE WAVELENGTHMx-ray1
2Toroidal focusing mirrorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97911
30.95371
40.97961
ReflectionResolution: 2.8→40.057 Å / Num. all: 9362 / Num. obs: 8420 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 22.7 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 70.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.8-2.9123.60.6846.10.6841,2100
2.91-3.0423.60.427100.4271,2100
3.04-3.223.60.26616.30.2661,2100
3.2-3.423.40.16525.80.1651,2100
3.4-3.6623.30.09341.90.0931,2100
3.66-4.0323.20.0659.40.061,2100
4.03-4.6222.80.0570.30.051,2100
4.62-5.81220.05973.30.0591,2100
5.81-50190.03600.031,2100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.8068→40.057 Å / SU ML: 0.31 / σ(F): 1.35 / Phase error: 27.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.259 418 5.01 %random 5%
Rwork0.2074 ---
obs0.21 8350 99.57 %-
all-9362 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8068→40.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1614 0 10 23 1647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081655
X-RAY DIFFRACTIONf_angle_d1.1052246
X-RAY DIFFRACTIONf_dihedral_angle_d17.682583
X-RAY DIFFRACTIONf_chiral_restr0.077266
X-RAY DIFFRACTIONf_plane_restr0.005287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8068-3.21280.33041350.21272573X-RAY DIFFRACTION100
3.2128-4.04720.25161380.21472596X-RAY DIFFRACTION100
4.0472-40.06060.24981450.20312763X-RAY DIFFRACTION99
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)
19.40831.0622-0.99383.96293.20993.8840.49190.15080.22910.0428-0.3575-0.0486-0.52110.5032-0.18680.6831-0.0965-0.12380.62620.26090.722-25.211735.66953.0416
29.39387.8519-3.20977.4412-2.53586.14110.17880.1901-0.0743-0.63840.25950.71880.6789-0.2873-0.41790.7040.0932-0.2190.66120.12630.6718-32.869222.20284.0883
37.3059-6.0537-5.90638.63664.20844.897-0.1596-0.2456-0.80990.0112-0.34941.18250.0081-0.68360.12170.79080.52010.18761.91310.79521.5901-49.224226.168418.255
46.92267.749-0.69289.7778-2.41852.50190.36-2.72390.36931.1962-0.23170.75080.6558-1.95870.06381.37090.07880.51711.9392-0.1580.8432-49.322531.8725.9722
53.42171.0763-3.0164.5321-3.37126.88930.2941-0.23550.23960.2303-0.01440.6002-0.535-0.4186-0.26740.49640.0253-0.14890.72360.11290.68-39.657928.859210.7707
67.8309-7.7104-1.98749.11473.88438.2475-0.9838-0.5431-1.15421.2991.36872.03910.6691.0768-0.06320.93610.1035-0.02580.87610.18681.0042-8.530328.7814-18.1258
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 7:58
2X-RAY DIFFRACTION2chain A and resid 59:86
3X-RAY DIFFRACTION3chain A and resid 87:93
4X-RAY DIFFRACTION4chain A and resid 94:99
5X-RAY DIFFRACTION5chain A and resid 100:212
6X-RAY DIFFRACTION6chain A and resid 213:229

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