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- PDB-3w1g: Crystal Structure of Human DNA ligase IV-Artemis Complex (Native) -

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Basic information

Entry
Database: PDB / ID: 3w1g
TitleCrystal Structure of Human DNA ligase IV-Artemis Complex (Native)
Components
  • Artemis-derived peptide
  • DNA ligase 4
KeywordsLIGASE / DNA ligase / non homologous end joining / DNA repair / XRCC4
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 / 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 / DNA repair metallo-beta-lactamase / DNA repair metallo-beta-lactamase / 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 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 / Protein artemis
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsOchi, 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
DepositionNov 15, 2012Deposition 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: Artemis-derived peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,93918
Polymers70,9912
Non-polymers1,94816
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-208 kcal/mol
Surface area26590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.260, 105.480, 121.080
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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


Mass: 69538.312 Da / Num. of mol.: 1 / 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: Protein/peptide Artemis-derived peptide / DNA cross-link repair 1C protein / Protein A-SCID / SNM1 homolog C / hSNM1C / SNM1-like protein


Mass: 1452.653 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96SD1
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 59.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2M ammonium sulfate, 10mM YCl, 100mM MES, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2012
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.55→68.26 Å / Num. all: 28941 / Num. obs: 27784 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Biso Wilson estimate: 46.91 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 8.8
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.562 / Mean I/σ(I) obs: 2 / % possible all: 97.5

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Processing

Software
NameVersionClassification
DNAdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3W1B

3w1b


Resolution: 2.55→59.462 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.33 / σ(F): 1.35 / Phase error: 23.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1388 5 %
Rwork0.18 --
obs0.1827 27757 95.01 %
all-29214 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.26 Å2 / Biso mean: 59.456 Å2 / Biso min: 22.45 Å2
Refinement stepCycle: LAST / Resolution: 2.55→59.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4623 0 106 71 4800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084823
X-RAY DIFFRACTIONf_angle_d1.1536540
X-RAY DIFFRACTIONf_dihedral_angle_d16.3221748
X-RAY DIFFRACTIONf_chiral_restr0.077728
X-RAY DIFFRACTIONf_plane_restr0.004812
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.64120.33961390.26642647278697
2.6412-2.74690.31871380.24312623276197
2.7469-2.87190.30211400.22642658279897
2.8719-3.02330.29261390.22212641278096
3.0233-3.21270.26991400.20572648278896
3.2127-3.46080.25691380.18752635277396
3.4608-3.8090.23071400.16562659279995
3.809-4.360.20791390.14342631277095
4.36-5.49260.16741370.14282602273993
5.4926-59.47790.20831380.18272625276389
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)
13.1863-1.6427-0.11574.02760.50142.36590.08520.1404-0.0141-0.07010.0739-0.0007-0.05820.0534-0.14360.3214-0.0048-0.04120.30050.01960.22889.445428.0532174.7169
21.72570.21390.92151.3352-0.90994.45990.12320.0939-0.1485-0.12820.0395-0.34040.52540.6486-0.15040.42250.1007-0.03610.4388-0.13230.405918.766512.4266143.8409
35.14041.3104-0.37331.6803-1.18175.02910.15820.03640.8039-0.0026-0.0458-0.2325-0.30110.3126-0.13490.35570.02350.14080.3623-0.070.72621.098234.8282119.3496
47.8362-6.38553.88735.9824-4.38943.8478-0.9209-0.04120.69570.86130.023-0.1314-1.14140.84160.84450.7277-0.0155-0.16420.82520.03380.413912.03622.1796193.0496
58.4913-7.88226.87337.8786-6.61465.6612-0.56860.6443-0.91880.4949-0.05220.6934-0.6747-0.60510.61390.7553-0.0721-0.03770.9445-0.03381.449621.322222.1853144.377
60.5636-0.13320.94030.0959-0.39351.8606-0.040.0767-0.09160.0565-0.1351-0.21380.63760.35880.20441.21740.0524-0.05070.9231-0.1551.363712.114821.5481144.9984
7-0.0403-0.0083-0.00430.0744-0.11180.0723-0.0109-0.0139-0.0205-0.03630.1287-0.0118-0.0248-0.1095-00.4690.02020.02950.4072-0.00160.389112.202524.9769156.2592
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and resseq 6:241A6 - 241
2X-RAY DIFFRACTION2chain A and resseq 242:454A242 - 454
3X-RAY DIFFRACTION3chain A and resseq 455:604A455 - 604
4X-RAY DIFFRACTION4chain BB486 - 495
5X-RAY DIFFRACTION5chain A and resseq 701:701A701
6X-RAY DIFFRACTION6chain A and resseq 702:716A702 - 716
7X-RAY DIFFRACTION7chain A and resseq 801:871A801 - 871

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