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- PDB-3rwr: Crystal structure of the human XRCC4-XLF complex -

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Basic information

Entry
Database: PDB / ID: 3rwr
TitleCrystal structure of the human XRCC4-XLF complex
Components
  • DNA repair protein XRCC4
  • Non-homologous end-joining factor 1
KeywordsDNA binding protein/protein binding / complex-filament / non-homologous end-joining / DNA and Protein Binding / 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 / 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
Helix hairpin bin / 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 / 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 ...Helix hairpin bin / 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 / 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 / Beta Complex / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
HEXATANTALUM DODECABROMIDE / DNA repair protein XRCC4 / Non-homologous end-joining factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 3.943 Å
AuthorsAndres, S.N. / Junop, M.S.
CitationJournal: To be Published
Title: Structure of human XLF-XRCC4: assembly of a functional DNA repair complex
Authors: Andres, N.S. / Wyman, C. / Modesti, M. / Junop, M.S.
History
DepositionMay 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Structure summary
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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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
D: Non-homologous end-joining factor 1
E: Non-homologous end-joining factor 1
F: DNA repair protein XRCC4
G: DNA repair protein XRCC4
H: Non-homologous end-joining factor 1
I: Non-homologous end-joining factor 1
J: DNA repair protein XRCC4
K: DNA repair protein XRCC4
L: Non-homologous end-joining factor 1
M: Non-homologous end-joining factor 1
N: DNA repair protein XRCC4
P: DNA repair protein XRCC4
O: Non-homologous end-joining factor 1
Q: Non-homologous end-joining factor 1
R: DNA repair protein XRCC4
V: DNA repair protein XRCC4
S: Non-homologous end-joining factor 1
W: Non-homologous end-joining factor 1
T: Non-homologous end-joining factor 1
X: Non-homologous end-joining factor 1
U: DNA repair protein XRCC4
Y: DNA repair protein XRCC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)558,22232
Polymers541,86624
Non-polymers16,3568
Water0
1
A: DNA repair protein XRCC4
B: DNA repair protein XRCC4
D: Non-homologous end-joining factor 1
E: Non-homologous end-joining factor 1
F: DNA repair protein XRCC4
G: DNA repair protein XRCC4
H: Non-homologous end-joining factor 1
I: Non-homologous end-joining factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,71110
Polymers180,6228
Non-polymers4,0892
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)745.379, 149.585, 80.475
Angle α, β, γ (deg.)90.00, 94.72, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a filament of alternating homodimers of XRCC4 and XLF. The unit is assembled by the following chains: GF, IH, BA, ED. This has been confirmed by SAXS (Hammel, M., Yu, Y., Fang, S., Lees-Miller, S.P., and Tainer, J.A. (2010). XLF regulates filament architecture of the XRCC4-ligaseIV complex. Structure. 11, 1431-1442.).

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Components

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


Mass: 18869.123 Da / Num. of mol.: 12 / Fragment: unp residues 1-157
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q13426
#2: Protein
Non-homologous end-joining factor 1 / Protein cernunnos / XRCC4-like factor


Mass: 26286.348 Da / Num. of mol.: 12 / Fragment: unp residues 1-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NHEJ1, XLF / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9H9Q4
#3: Chemical
ChemComp-TBR / HEXATANTALUM DODECABROMIDE / DODECABROMOHEXATANTALUM


Mass: 2044.535 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br12Ta6

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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: 4.13 Å3/Da / Density % sol: 70.19 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1.8M Ammonium citrate, pH 8.0, 20 mM Barium chloride dihydrate, 400 mM sodium thiocyanate, 0.5 mM tantalum bromide, 60% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.2536 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 24, 2010
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2536 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. all: 78630 / Num. obs: 78630 / % possible obs: 97.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 3.9→4.2 Å / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX1.7.2_869refinement
PHENIXmodel building
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
CBASSdata collection
RefinementMethod to determine structure: molecular replacement-SAD / Resolution: 3.943→49.027 Å / SU ML: 1.55 / σ(F): 0 / Phase error: 36.08 / Stereochemistry target values: MLHL
Details: THE TA ATOM FOR CHAINS P AND V HAS BEEN REFINED WITH OCCUPANCY HIGHER THAN 1.0.
RfactorNum. reflection% reflection
Rfree0.3256 3879 5.03 %
Rwork0.2707 --
obs0.2735 77191 99.14 %
all-77252 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 157.435 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--58.2565 Å20 Å2-37.7716 Å2
2--44.8642 Å2-0 Å2
3---13.3923 Å2
Refinement stepCycle: LAST / Resolution: 3.943→49.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36689 0 144 0 36833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00337747
X-RAY DIFFRACTIONf_angle_d0.78850670
X-RAY DIFFRACTIONf_dihedral_angle_d19.5313882
X-RAY DIFFRACTIONf_chiral_restr0.0655660
X-RAY DIFFRACTIONf_plane_restr0.0036519
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9427-3.99070.4165950.39312157X-RAY DIFFRACTION81
3.9907-4.04120.41491510.38092644X-RAY DIFFRACTION100
4.0412-4.09440.40661390.36212532X-RAY DIFFRACTION100
4.0944-4.15040.42851370.35562683X-RAY DIFFRACTION100
4.1504-4.20970.37811230.32872624X-RAY DIFFRACTION100
4.2097-4.27250.35451520.32232631X-RAY DIFFRACTION100
4.2725-4.33920.35551340.29152557X-RAY DIFFRACTION100
4.3392-4.41030.31341280.26712660X-RAY DIFFRACTION100
4.4103-4.48630.33181360.25912696X-RAY DIFFRACTION100
4.4863-4.56780.32091200.26022602X-RAY DIFFRACTION100
4.5678-4.65560.29491260.23762615X-RAY DIFFRACTION100
4.6556-4.75060.31811490.24492665X-RAY DIFFRACTION100
4.7506-4.85380.31341280.23792590X-RAY DIFFRACTION100
4.8538-4.96660.28961340.24422647X-RAY DIFFRACTION100
4.9666-5.09070.32691440.24982613X-RAY DIFFRACTION100
5.0907-5.22810.31291230.2522642X-RAY DIFFRACTION100
5.2281-5.38180.39891500.27872681X-RAY DIFFRACTION100
5.3818-5.55530.39481440.34022573X-RAY DIFFRACTION100
5.5553-5.75350.44651640.3672665X-RAY DIFFRACTION100
5.7535-5.98350.38531400.35582584X-RAY DIFFRACTION100
5.9835-6.25530.40251480.36762677X-RAY DIFFRACTION100
6.2553-6.58440.43781460.35942611X-RAY DIFFRACTION100
6.5844-6.99580.38421260.32762640X-RAY DIFFRACTION100
6.9958-7.53420.40061420.28132667X-RAY DIFFRACTION100
7.5342-8.28910.27351700.21022630X-RAY DIFFRACTION100
8.2891-9.48110.22291450.16662665X-RAY DIFFRACTION100
9.4811-11.91670.20291500.17142637X-RAY DIFFRACTION99
11.9167-49.03040.3371350.30112724X-RAY DIFFRACTION99

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