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- PDB-3w5o: Crystal Structure of Human DNA ligase IV -

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Basic information

Entry
Database: PDB / ID: 3w5o
TitleCrystal Structure of Human DNA ligase IV
ComponentsDNA ligase 4
KeywordsLIGASE / DNA ligase / non homologous end joining / DNA repair / XRCC4 / Artemis
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 / DNA ligase/mRNA capping enzyme / 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 / D-amino Acid Aminotransferase; Chain A, domain 1 / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / DNA ligase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsGu, X. / Ochi, T. / Blundell, T.L.
CitationJournal: Structure / Year: 2013
Title: Structure of the catalytic region of DNA ligase IV in complex with an artemis fragment sheds light on double-strand break repair
Authors: Ochi, T. / Gu, X. / Blundell, T.L.
History
DepositionFeb 2, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Nov 8, 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 / 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 / _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 ligase 4
B: DNA ligase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,39628
Polymers139,0772
Non-polymers3,32026
Water50428
1
A: DNA ligase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,29415
Polymers69,5381
Non-polymers1,75614
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA ligase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,10213
Polymers69,5381
Non-polymers1,56412
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.290, 104.360, 120.040
Angle α, β, γ (deg.)90.00, 94.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 69538.312 Da / Num. of mol.: 2 / Fragment: catalytic region, UNP residues 1-609
Source method: isolated from a genetically manipulated source
Details: Hippocampus / Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Plasmid: pOPINS / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)pLysS / References: UniProt: P49917, DNA ligase (ATP)
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3.07 Å3/Da / Density % sol: 59.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 2M ammonium sulfate, 10mM YCl, 100mM MES, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.84→200 Å / Num. all: 39997 / Num. obs: 39757 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 10.1
Reflection shellResolution: 2.84→2.91 Å / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2904 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3W1B

3w1b


Resolution: 2.84→47.835 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2455 1976 4.97 %random
Rwork0.1935 ---
all0.1961 39983 --
obs0.1961 39732 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.4298 Å2
Refinement stepCycle: LAST / Resolution: 2.84→47.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8793 0 182 28 9003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099141
X-RAY DIFFRACTIONf_angle_d1.25212435
X-RAY DIFFRACTIONf_dihedral_angle_d16.0593237
X-RAY DIFFRACTIONf_chiral_restr0.0771409
X-RAY DIFFRACTIONf_plane_restr0.0071561
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.835-2.90590.33561390.25082656100
2.9059-2.98450.28941370.23152727100
2.9845-3.07230.28331380.2312668100
3.0723-3.17140.28571430.21212680100
3.1714-3.28480.31121370.2028271799
3.2848-3.41630.24531420.18632684100
3.4163-3.57170.27591500.18512679100
3.5717-3.75990.25741360.18270699
3.7599-3.99540.21871360.1811269999
3.9954-4.30370.20561420.1623270399
4.3037-4.73640.22191460.1649267399
4.7364-5.4210.23251450.1821268299
5.421-6.82670.28541400.2242753100
6.8267-47.84180.21021450.2129272998
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)
12.65951.37990.42863.69990.53912.46960.04050.0241-0.0185-0.0714-0.0668-0.0973-0.10860.04950.02780.3618-0.02550.04650.35410.02450.2681-23.423720.8218-23.3267
23.3205-0.822-0.14132.6309-1.6764.96650.01220.1131-0.04030.1959-0.0245-0.2015-0.5662-0.05350.00110.4827-0.0736-0.00730.2712-0.020.3216-16.507837.08397.3846
32.9539-0.6704-0.54013.4592-0.52875.7425-0.139-0.1853-0.19970.04740.0005-0.23470.26650.09540.08770.2434-0.029-0.04720.31750.03220.4597-15.07313.509132.11
43.4794-1.5391-0.15334.31490.27862.88010.0108-0.06620.02870.15950.0846-0.1924-0.0150.0682-0.09650.2867-0.0213-0.01560.38970.01790.2587-22.2399-28.6056-35.265
52.73031.29710.39361.8519-1.70886.05880.042-0.0837-0.089-0.0606-0.0456-0.14790.41990.16860.00360.41980.07270.03330.3158-0.0740.3639-10.9571-45.0404-64.791
63.16880.6542-0.69942.3305-1.12434.38550.0881-0.05990.3505-0.0284-0.059-0.0612-0.40380.1539-0.03680.37030.01780.07640.2887-0.04170.478-5.3017-21.8951-89.6814
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 8:240A8 - 240
2X-RAY DIFFRACTION2chain A and resseq 241:453A241 - 453
3X-RAY DIFFRACTION3chain A and resseq 461:603A461 - 603
4X-RAY DIFFRACTION4chain B and resseq 8:240B8 - 240
5X-RAY DIFFRACTION5chain B and resseq 241:453B241 - 453
6X-RAY DIFFRACTION6chain B and resseq 460:603B460 - 603

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