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- PDB-3ii6: Structure of human Xrcc4 in complex with the tandem BRCT domains ... -

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Basic information

Entry
Database: PDB / ID: 3ii6
TitleStructure of human Xrcc4 in complex with the tandem BRCT domains of DNA LigaseIV.
Components
  • DNA ligase 4
  • DNA repair protein XRCC4
KeywordsLIGASE/DNA BINDING PROTEIN / XRCC4 / DNA LIGASE IV / NHEJ / DNA REPAIR / BRCT / Alternative splicing / Coiled coil / DNA damage / DNA recombination / Isopeptide bond / Nucleus / Phosphoprotein / Polymorphism / Ubl conjugation / ATP-binding / Cell cycle / Cell division / Disease mutation / DNA replication / Ligase / Magnesium / Metal-binding / Nucleotide-binding / SCID / LIGASE-DNA BINDING PROTEIN COMPLEX
Function / homology
Function and homology information


DNA ligation involved in DNA recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / 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 ...DNA ligation involved in DNA recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / 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 / protein localization to site of double-strand break / 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 / SUMOylation of DNA damage response and repair proteins / 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 / site of double-strand break / 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 / identical protein binding / nucleus / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #520 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #520 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #370 / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / XRCC4 N-terminal domain / XRCC4-like, N-terminal domain superfamily / 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. / BRCT domain / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / DNA repair protein XRCC4-like, C-terminal / BRCA1 C Terminus (BRCT) domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Beta Complex / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Nucleic acid-binding, OB-fold / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA ligase 4 / DNA repair protein XRCC4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsMeesala, S. / Junop, M.
CitationJournal: MOL.CELL.BIOL. / Year: 2009
Title: Structural and functional interaction between the human DNA repair proteins DNA ligase IV and XRCC4
Authors: Wu, P.Y. / Frit, P. / Meesala, S. / Dauvillier, S. / Modesti, M. / Andres, S.N. / Huang, Y. / Sekiguchi, J. / Calsou, P. / Salles, B. / Junop, M.S.
History
DepositionJul 31, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein XRCC4
B: DNA repair protein XRCC4
C: DNA repair protein XRCC4
D: DNA repair protein XRCC4
X: DNA ligase 4
Y: DNA ligase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,2128
Polymers154,1416
Non-polymers712
Water5,062281
1
A: DNA repair protein XRCC4
B: DNA repair protein XRCC4
X: DNA ligase 4


Theoretical massNumber of molelcules
Total (without water)77,0703
Polymers77,0703
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9800 Å2
ΔGint-82 kcal/mol
Surface area34800 Å2
MethodPISA
2
C: DNA repair protein XRCC4
D: DNA repair protein XRCC4
Y: DNA ligase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,1415
Polymers77,0703
Non-polymers712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-95 kcal/mol
Surface area35090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.243, 85.982, 111.608
Angle α, β, γ (deg.)67.34, 82.86, 74.52
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
DNA repair protein XRCC4 / X-ray repair cross-complementing protein 4


Mass: 23424.537 Da / Num. of mol.: 4 / Fragment: residues 1-203 / Mutation: A60E, I134T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4 / Plasmid: pACYC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13426
#2: Protein DNA ligase 4 / DNA ligase IV / Polydeoxyribonucleotide synthase [ATP] 4


Mass: 30221.357 Da / Num. of mol.: 2 / Fragment: C-Terminal tandem BRCT domains, residues 654-911
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIG4 / Plasmid: pPROEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P49917, DNA ligase (ATP)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 3.72 Å3/Da / Density % sol: 66.95 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM Sodium/Potassium phosphate, 15% PEG 8000 MME, 200mM Sodium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 28, 2005 / Details: parabolic collimating mirror
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.29→45.43 Å / Num. all: 98177 / Num. obs: 96105 / % possible obs: 97.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.79 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 12
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 2.75 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.7 / % possible all: 96

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Processing

Software
NameClassification
CNSrefinement
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→20 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 5334 -RANDOM
Rwork0.24 ---
obs0.24 83736 86.9 %-
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10642 0 2 281 10925
Xplor file
Refine-IDSerial noTopol file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param

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