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- PDB-3sr2: Crystal Structure of Human XLF-XRCC4 Complex -

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Basic information

Entry
Database: PDB / ID: 3sr2
TitleCrystal Structure of Human XLF-XRCC4 Complex
Components
  • DNA repair protein XRCC4
  • Non-homologous end-joining factor 1
KeywordsDNA BINDING PROTEIN/PROTEIN BINDING / XRCC4 / XLF / NHEJ / DNA Repair / DNA / DNA Ligases / DNA-Binding Proteins / Dimerization / Humans / Protein Structure / Quaternary / Complex / Non-Homologous End Joining (NHEJ) / DNA ligase IV / Ku / XLF-XRCC4 / Protein DNA-interaction / DNA BINDING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


FHA domain binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA end binding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / response to ionizing radiation ...FHA domain binding / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA end binding / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / response to ionizing radiation / cellular response to lithium ion / 2-LTR circle formation / T cell differentiation / response to X-ray / DNA polymerase binding / SUMOylation of DNA damage response and repair proteins / B cell differentiation / central nervous system development / Nonhomologous End-Joining (NHEJ) / fibrillar center / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Helix hairpin bin / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XLF, N-terminal / XLF-Cernunnos, XRcc4-like factor, NHEJ component / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / DNA double-strand break repair and V(D)J recombination protein XRCC4 / XRCC4-like, N-terminal domain superfamily / DNA repair protein XRCC4-like, C-terminal ...Helix hairpin bin / DNA double-strand break repair and VJ recombination XRCC4, N-terminal / Dna Repair Protein Xrcc4; Chain: A, domain 1 / XLF, N-terminal / XLF-Cernunnos, XRcc4-like factor, NHEJ component / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / DNA double-strand break repair and V(D)J recombination protein XRCC4 / XRCC4-like, N-terminal domain superfamily / DNA repair protein XRCC4-like, C-terminal / Beta Complex / Helix Hairpins / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
DNA repair protein XRCC4 / Non-homologous end-joining factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9708 Å
AuthorsHammel, M. / Classen, S. / Tainer, J.A.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: XRCC4 Protein Interactions with XRCC4-like Factor (XLF) Create an Extended Grooved Scaffold for DNA Ligation and Double Strand Break Repair.
Authors: Hammel, M. / Rey, M. / Yu, Y. / Mani, R.S. / Classen, S. / Liu, M. / Pique, M.E. / Fang, S. / Mahaney, B.L. / Weinfeld, M. / Schriemer, D.C. / Lees-Miller, S.P. / Tainer, J.A.
History
DepositionJul 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Database references
Revision 1.2Sep 28, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA repair protein XRCC4
B: DNA repair protein XRCC4
C: Non-homologous end-joining factor 1
D: Non-homologous end-joining factor 1
E: DNA repair protein XRCC4
F: DNA repair protein XRCC4
G: Non-homologous end-joining factor 1
H: Non-homologous end-joining factor 1


Theoretical massNumber of molelcules
Total (without water)168,5018
Polymers168,5018
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: DNA repair protein XRCC4
B: DNA repair protein XRCC4


Theoretical massNumber of molelcules
Total (without water)32,5132
Polymers32,5132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-18 kcal/mol
Surface area15150 Å2
MethodPISA
3
C: Non-homologous end-joining factor 1
D: Non-homologous end-joining factor 1


Theoretical massNumber of molelcules
Total (without water)51,7382
Polymers51,7382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6700 Å2
ΔGint-65 kcal/mol
Surface area23010 Å2
MethodPISA
4
E: DNA repair protein XRCC4
F: DNA repair protein XRCC4


Theoretical massNumber of molelcules
Total (without water)32,5132
Polymers32,5132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-19 kcal/mol
Surface area15340 Å2
MethodPISA
5
G: Non-homologous end-joining factor 1
H: Non-homologous end-joining factor 1


Theoretical massNumber of molelcules
Total (without water)51,7382
Polymers51,7382
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6850 Å2
ΔGint-62 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.017, 110.017, 763.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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


Mass: 16256.343 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: Q13426
#2: Protein
Non-homologous end-joining factor 1 / Protein cernunnos / XRCC4-like factor


Mass: 25868.922 Da / Num. of mol.: 4 / Fragment: UNP Residues 1-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHEJ1, XLF / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: Q9H9Q4

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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: 3.96 Å3/Da / Density % sol: 68.93 %
Crystal growTemperature: 303.15 K / Method: vapor diffusion / pH: 7
Details: protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, ...Details: protein combined with equal volumes of 100 mM HEPES, pH 7.8, 13% (w/v) PEG 3350, 300 mM NaCl, 2 mM ADP, 7 mM NaF and 3 mM BeCl) and then dehydrated over 1000 ul of 19% PEG 3350, 300 mM NaCl, 100 mM HEPES, pH7.8 under argon., vapor diffusion, temperature 303.15K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 3.9→70 Å / Num. all: 26221 / Num. obs: 26221 / % possible obs: 98.8 % / Observed criterion σ(I): 1.7 / Redundancy: 23.8 % / Rmerge(I) obs: 0.131 / Χ2: 1.098 / Net I/σ(I): 2.6
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
3.9-3.9721.611431.026188.7
3.97-4.0423.812651.033199.7
4.04-4.1224.912501.034199.8
4.12-4.22513091.122199.7
4.2-4.2924.812541.046199.7
4.29-4.3924.913161.104199.7
4.39-4.524.912481.146199.7
4.5-4.6224.613011.188199.6
4.62-4.7624.813121.26199.7
4.76-4.9124.812601.341199.6
4.91-5.0924.513011.255199.5
5.09-5.2924.513151.279199.5
5.29-5.5324.313071.382199.6
5.53-5.8324.413210.83911000.912
5.83-6.1923.813360.80611000.787
6.19-6.6724.113190.817199.80.593
6.67-7.3423.513840.81811000.368
7.34-8.423.213700.893199.90.186
8.4-10.5721.814031.113198.90.103
10.57-7018.615071.4891940.067

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R9A

2r9a


Resolution: 3.9708→67.436 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.5821 / SU ML: 0.92 / σ(F): 0.24 / Phase error: 43.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.369 1704 7.82 %
Rwork0.3577 --
obs0.3586 21777 86.52 %
all-26221 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.293 e/Å3
Displacement parametersBiso max: 80 Å2 / Biso mean: 80 Å2 / Biso min: 80 Å2
Baniso -1Baniso -2Baniso -3
1-180.3722 Å2-0 Å20 Å2
2--180.3722 Å2-0 Å2
3---62.6117 Å2
Refinement stepCycle: LAST / Resolution: 3.9708→67.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11363 0 0 0 11363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01812156
X-RAY DIFFRACTIONf_angle_d1.25615672
X-RAY DIFFRACTIONf_chiral_restr0.0781779
X-RAY DIFFRACTIONf_plane_restr0.0082000
X-RAY DIFFRACTIONf_dihedral_angle_d18.4674281
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.9708-4.08770.49741050.48831295140070
4.0877-4.21960.38961110.4561415152674
4.2196-4.37040.40951210.41281475159680
4.3704-4.54530.45911290.40251544167382
4.5453-4.75210.38211310.40621570170183
4.7521-5.00260.43011400.3991642178286
5.0026-5.31590.45831440.4061662180689
5.3159-5.72620.44731480.40041716186489
5.7262-6.3020.44471550.39411764191991
6.302-7.21310.40441620.37451852201495
7.2131-9.08420.3251700.3161969213998
9.0842-67.44550.25071880.26312169235799

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