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- PDB-3w03: XLF-XRCC4 complex -

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Basic information

Entry
Database: PDB / ID: 3w03
TitleXLF-XRCC4 complex
Components
  • DNA repair protein XRCC4
  • Non-homologous end-joining factor 1
KeywordsDNA BINDING PROTEIN / Coiled-Coil / NHEJ / DSBs repair / Ku70/80 / DNA-PKcs / DNA ligase IV
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 / SUMOylation of DNA damage response and repair proteins / DNA polymerase binding / 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
XLF, N-terminal / XLF N-terminal domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / XRCC4 N-terminal domain / XRCC4-like, N-terminal domain superfamily / DNA repair protein XRCC4-like, C-terminal
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: 8.492 Å
AuthorsWu, Q. / Ochi, T. / Matak-Vinkovic, D. / Robinson, C.V. / Chirgadze, D.Y. / Blundell, T.L.
CitationJournal: Biochem.Soc.Trans. / Year: 2011
Title: Non-homologous end-joining partners in a helical dance: structural studies of XLF-XRCC4 interactions
Authors: Wu, Q. / Ochi, T. / Matak-Vinkovic, D. / Robinson, C.V. / Chirgadze, D.Y. / Blundell, T.L.
History
DepositionOct 17, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,3934
Polymers95,3934
Non-polymers00
Water0
1
A: Non-homologous end-joining factor 1
B: Non-homologous end-joining factor 1


Theoretical massNumber of molelcules
Total (without water)53,2752
Polymers53,2752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-57 kcal/mol
Surface area22990 Å2
MethodPISA
2
C: DNA repair protein XRCC4
D: DNA repair protein XRCC4


Theoretical massNumber of molelcules
Total (without water)42,1172
Polymers42,1172
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-30 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)236.762, 236.762, 103.229
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Non-homologous end-joining factor 1 / Protein cernunnos / XRCC4-like factor


Mass: 26637.740 Da / Num. of mol.: 2 / Fragment: UNP residues 1-233
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHEJ1, XLF / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H9Q4
#2: Protein DNA repair protein XRCC4 / / X-ray repair cross-complementing protein 4


Mass: 21058.582 Da / Num. of mol.: 2 / Fragment: UNP residues 1-164
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13426

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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: 8.7556 Å3/Da / Density % sol: 85.9519 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M Tris pH7.5, 2M Sodium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2009
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 8.492→49.81 Å / Num. all: 3019 / Num. obs: 2995 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 926.75 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 12
Reflection shellResolution: 8.5→8.8 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.445 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(1.7.2_869)model building
PHENIX(1.7.2_869)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIX(1.7.2_869)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QM4, 1FU1

2qm4

1fu1


Resolution: 8.492→49.81 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.59 / SU ML: 2.57 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 44.29 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.3599 292 9.75 %Random
Rwork0.3627 ---
all0.3622 3019 --
obs0.3622 2995 99.34 %-
Solvent computationShrinkage radii: 1.11 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso max: 154.97 Å2 / Biso mean: 73.3344 Å2 / Biso min: 7.9 Å2
Baniso -1Baniso -2Baniso -3
1-1009.5581 Å2-0 Å20 Å2
2--1009.5581 Å2-0 Å2
3---705.0311 Å2
Refinement stepCycle: LAST / Resolution: 8.492→49.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6229 0 0 0 6229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166351
X-RAY DIFFRACTIONf_angle_d1.38587
X-RAY DIFFRACTIONf_dihedral_angle_d17.7512349
X-RAY DIFFRACTIONf_chiral_restr0.091962
X-RAY DIFFRACTIONf_plane_restr0.0051106
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
8.4917-10.68130.4271440.38421336X-RAY DIFFRACTION100
10.6813-49.8110.34351480.35691367X-RAY DIFFRACTION99
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)
10.6433-0.3597-0.62851.43130.20841.0335-0.0804-0.40880.98250.1210.23650.2438-0.39370.87290.6006-0.28880.0949-1.4733-0.56050.7818-0.038887.145739.59356.4403
20.6-0.0915-0.24520.2602-0.0270.1824-0.48960.6548-0.5987-0.21520.17880.71760.0929-0.9242-1.1310.0534-0.46240.2613-0.43591.0529-0.223990.480825.961425.7923
30.40290.08280.0171.28930.06161.04661.23190.51110.19850.09541.2438-0.7440.232-0.26913.46710.6664-0.14922.22730.28351.78550.819181.2454-16.9499-15.2972
40.27730.6570.2841.35820.54260.4227-0.22760.717-0.0255-0.34890.1434-1.1149-0.21390.1979-0.09041.60670.9568-1.3616-0.54981.98641.979880.1707-9.335-39.5108
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA0 - 230
2X-RAY DIFFRACTION2chain BB-1 - 227
3X-RAY DIFFRACTION3chain CC1 - 164
4X-RAY DIFFRACTION4chain DD1 - 164

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