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- PDB-3w1b: Crystal Structure of Human DNA ligase IV-Artemis Complex (Mercury... -

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Basic information

Entry
Database: PDB / ID: 3w1b
TitleCrystal Structure of Human DNA ligase IV-Artemis Complex (Mercury Derivative)
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 / DNA-dependent protein kinase-DNA ligase 4 complex / single strand break repair / single-stranded DNA endodeoxyribonuclease activity / 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 / 5'-3' DNA exonuclease activity / positive regulation of neurogenesis / nucleotide-excision repair, DNA gap filling / response to ionizing radiation / 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 / interstrand cross-link repair / condensed chromosome / telomere maintenance / B cell differentiation / 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 / endonuclease activity / neuron apoptotic process / adaptive immune response / in utero embryonic development / negative regulation of neuron apoptotic process / cell population proliferation / chromosome, telomeric region / damaged DNA binding / 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 MONOPHOSPHATE / : / DNA ligase 4 / Protein artemis
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 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 14, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references

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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)74,10422
Polymers70,9912
Non-polymers3,11320
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-326 kcal/mol
Surface area27430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.630, 105.210, 122.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#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

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Non-polymers , 4 types, 237 molecules

#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Hg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.1 Å3/Da / Density % sol: 60.36 %
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: 1.0036, 1.0093, 0.9915
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2012
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00361
21.00931
30.99151
ReflectionResolution: 2.4→59.82 Å / Num. all: 35180 / Num. obs: 34931 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 38.14 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 8.5
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 1.9 / Num. measured obs: 5069 / % possible all: 100

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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: MAD / Resolution: 2.4→59.82 Å / Occupancy max: 1 / Occupancy min: 0.4 / SU ML: 0.29 / σ(F): 1.35 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2253 1994 5.71 %
Rwork0.1763 --
obs0.1791 34921 98.93 %
all-35298 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 174.78 Å2 / Biso mean: 43.5842 Å2 / Biso min: 15.38 Å2
Refinement stepCycle: LAST / Resolution: 2.4→59.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 63 217 5003
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094868
X-RAY DIFFRACTIONf_angle_d1.1376580
X-RAY DIFFRACTIONf_dihedral_angle_d15.2461797
X-RAY DIFFRACTIONf_chiral_restr0.078726
X-RAY DIFFRACTIONf_plane_restr0.005832
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.460.31461430.249723502493100
2.46-2.52650.32421400.235623082448100
2.5265-2.60090.30371430.229423512494100
2.6009-2.68480.29571410.221623352476100
2.6848-2.78080.26611430.213223522495100
2.7808-2.89210.28061420.202223322474100
2.8921-3.02380.2681420.223482490100
3.0238-3.18320.25541420.1962337247999
3.1832-3.38260.22031430.17252350249399
3.3826-3.64370.21261430.15922348249199
3.6437-4.01030.21351420.15132356249899
4.0103-4.59050.17391440.13292364250898
4.5905-5.78280.18041400.15292350249096
5.7828-59.83850.19941460.18012446259296
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)
11.8592-1.01-0.19542.6799-0.18012.35820.01260.047-0.04220.02560.08880.01480.0436-0.0812-0.09760.1883-0.01670.00310.2128-0.01470.1806-9.562224.48453.6488
21.69610.0888-0.45212.13441.3084.56120.14630.033-0.0037-0.0783-0.03540.1569-0.4159-0.625-0.09740.31070.07680.0390.35650.1050.2725-19.050639.799722.4208
35.41620.34290.06931.50390.43242.79960.1503-0.1728-0.6615-0.0132-0.03640.10970.2993-0.1946-0.09050.2579-0.0028-0.0760.27830.04850.4352-21.055317.197-2.3832
48.503-6.6887-3.45885.34862.99042.5231-0.2229-0.57310.33191.31360.1606-0.61430.6278-0.57340.09860.65370.01630.06840.6405-0.00510.4345-11.878331.141772.053
51.296-0.4633-0.67520.80790.6050.5291-0.0573-0.14230.1658-0.1634-0.04420.1680.1731-0.02830.10550.6999-0.005-0.0510.82020.09630.6398-11.486331.551231.3755
6-0.1810.0326-0.067-0.0840.13960.29980.04150.0396-0.06050.00590.02240.0565-0.088-0.0981-0.06250.25410.05630.04080.310.02190.2904-14.129528.818534.2651
7-0.22330.06980.43361.62550.16240.379-0.1761-0.1084-0.2778-0.310.14160.2252-0.3411-0.18530.02780.49440.00820.1290.9738-0.02780.7427-14.647723.870612.541
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 242:454 or chain A and resseq 701:701A242 - 454
3X-RAY DIFFRACTION2chain A and resseq 242:454 or chain A and resseq 701:701A701
4X-RAY DIFFRACTION3chain A and resseq 455:604A455 - 605
5X-RAY DIFFRACTION4chain B and resseq 486:495B486 - 495
6X-RAY DIFFRACTION5chain A and resseq 702:711A702 - 711
7X-RAY DIFFRACTION6chain A and resseq 801:1016 or chain B and resseq 501:501A801 - 1016
8X-RAY DIFFRACTION6chain A and resseq 801:1016 or chain B and resseq 501:501B501
9X-RAY DIFFRACTION7chain A and resseq 712:720A712 - 720

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