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- PDB-6erg: Complex of XLF and heterodimer Ku bound to DNA -

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Basic information

Entry
Database: PDB / ID: 6erg
TitleComplex of XLF and heterodimer Ku bound to DNA
Components
  • (X-ray repair cross-complementing protein ...) x 2
  • DNA (21-MER)
  • DNA (34-MER)
  • Non-homologous end-joining factor 1
KeywordsDNA BINDING PROTEIN / DNA repair complex NHEJ
Function / homology
Function and homology information


positive regulation of ligase activity / DNA ligase IV complex / Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination ...positive regulation of ligase activity / DNA ligase IV complex / Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / regulation of smooth muscle cell proliferation / cellular response to X-ray / nuclear telomere cap complex / double-strand break repair via classical nonhomologous end joining / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / positive regulation of neurogenesis / recombinational repair / regulation of telomere maintenance / protein localization to chromosome, telomeric region / U3 snoRNA binding / cellular hyperosmotic salinity response / response to ionizing radiation / 2-LTR circle formation / telomeric DNA binding / hematopoietic stem cell proliferation / positive regulation of protein kinase activity / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / site of DNA damage / T cell differentiation / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / DNA polymerase binding / neurogenesis / telomere maintenance / activation of innate immune response / DNA helicase activity / cyclin binding / cellular response to leukemia inhibitory factor / B cell differentiation / central nervous system development / small-subunit processome / Nonhomologous End-Joining (NHEJ) / enzyme activator activity / cellular response to gamma radiation / protein-DNA complex / double-strand break repair via nonhomologous end joining / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / fibrillar center / double-strand break repair / site of double-strand break / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA recombination / transcription regulator complex / ficolin-1-rich granule lumen / damaged DNA binding / chromosome, telomeric region / transcription cis-regulatory region binding / ribonucleoprotein complex / innate immune response / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of DNA-templated transcription / protein-containing complex binding / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / nucleus / membrane / plasma membrane / cytosol
Similarity search - Function
Ku70, bridge and pillars / Ku70, bridge and pillars / Ku70; Chain: A; Domain 2 - #10 / Ku70; Chain: A; Domain 2 / Ku70; Chain: A; domain 4 / Ku70; Chain: A; domain 4 - #10 / XLF, N-terminal / : / : / XLF N-terminal domain ...Ku70, bridge and pillars / Ku70, bridge and pillars / Ku70; Chain: A; Domain 2 - #10 / Ku70; Chain: A; Domain 2 / Ku70; Chain: A; domain 4 / Ku70; Chain: A; domain 4 - #10 / XLF, N-terminal / : / : / XLF N-terminal domain / XLF protein coiled-coil region / XRCC4-like, N-terminal domain superfamily / Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / von Willebrand factor, type A domain / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Few Secondary Structures / Irregular / Beta Barrel / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / X-ray repair cross-complementing protein 6 / X-ray repair cross-complementing protein 5 / Non-homologous end-joining factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsNemoz, C. / Legrand, P. / Ropars, V. / Charbonnier, J.B.
Funding support France, 2items
OrganizationGrant numberCountry
INCAPLBIO 2012-280 France
French National Research AgencyANR-12-SVSE8-012 France
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2018
Title: XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining.
Authors: Nemoz, C. / Ropars, V. / Frit, P. / Gontier, A. / Drevet, P. / Yu, J. / Guerois, R. / Pitois, A. / Comte, A. / Delteil, C. / Barboule, N. / Legrand, P. / Baconnais, S. / Yin, Y. / Tadi, S. / ...Authors: Nemoz, C. / Ropars, V. / Frit, P. / Gontier, A. / Drevet, P. / Yu, J. / Guerois, R. / Pitois, A. / Comte, A. / Delteil, C. / Barboule, N. / Legrand, P. / Baconnais, S. / Yin, Y. / Tadi, S. / Barbet-Massin, E. / Berger, I. / Le Cam, E. / Modesti, M. / Rothenberg, E. / Calsou, P. / Charbonnier, J.B.
History
DepositionOct 18, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 17, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen / pdbx_seq_map_depositor_info
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 17, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: X-ray repair cross-complementing protein 6
B: X-ray repair cross-complementing protein 5
C: Non-homologous end-joining factor 1
D: X-ray repair cross-complementing protein 6
E: X-ray repair cross-complementing protein 5
F: Non-homologous end-joining factor 1
H: DNA (21-MER)
K: DNA (21-MER)
M: DNA (34-MER)
R: DNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)292,99913
Polymers292,71010
Non-polymers2883
Water36020
1
A: X-ray repair cross-complementing protein 6
B: X-ray repair cross-complementing protein 5
F: Non-homologous end-joining factor 1
H: DNA (21-MER)
R: DNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,4516
Polymers146,3555
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27130 Å2
ΔGint-173 kcal/mol
Surface area55170 Å2
MethodPISA
2
C: Non-homologous end-joining factor 1
D: X-ray repair cross-complementing protein 6
E: X-ray repair cross-complementing protein 5
K: DNA (21-MER)
M: DNA (34-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,5477
Polymers146,3555
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27680 Å2
ΔGint-182 kcal/mol
Surface area55470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.710, 114.260, 127.170
Angle α, β, γ (deg.)90.000, 93.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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X-ray repair cross-complementing protein ... , 2 types, 4 molecules ADBE

#1: Protein X-ray repair cross-complementing protein 6 / 5'-deoxyribose-5-phosphate lyase Ku70 / 5'-dRP lyase Ku70 / 70 kDa subunit of Ku antigen / ATP- ...5'-deoxyribose-5-phosphate lyase Ku70 / 5'-dRP lyase Ku70 / 70 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 1 / ATP-dependent DNA helicase II 70 kDa subunit / CTC box-binding factor 75 kDa subunit / CTCBF / DNA repair protein XRCC6 / Lupus Ku autoantigen protein p70 / Ku70 / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 6


Mass: 62629.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC6, G22P1 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P12956, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#2: Protein X-ray repair cross-complementing protein 5 / 86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase ...86 kDa subunit of Ku antigen / ATP-dependent DNA helicase 2 subunit 2 / ATP-dependent DNA helicase II 80 kDa subunit / CTC box-binding factor 85 kDa subunit / CTCBF / DNA repair protein XRCC5 / Ku80 / Ku86 / Lupus Ku autoantigen protein p86 / Nuclear factor IV / Thyroid-lupus autoantigen / TLAA / X-ray repair complementing defective repair in Chinese hamster cells 5 (double-strand-break rejoining)


Mass: 65356.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XRCC5, G22P2 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P13010, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement

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Protein/peptide , 1 types, 2 molecules CF

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


Mass: 1536.907 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H9Q4

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DNA chain , 2 types, 4 molecules HKMR

#4: DNA chain DNA (21-MER)


Mass: 6506.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)
#5: DNA chain DNA (34-MER)


Mass: 10325.685 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Synthetic construct (others)

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Non-polymers , 2 types, 23 molecules

#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.75 Å3/Da / Density % sol: 55.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 18% PEG 3350, 150 mM Na sulfate , 100 mM Bis-Tris-Propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98009 Å / Relative weight: 1
ReflectionResolution: 2.9→48.76 Å / Num. obs: 51644 / % possible obs: 72.9 % / Redundancy: 14 % / Biso Wilson estimate: 106.46 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.068 / Rrim(I) all: 0.182 / Net I/σ(I): 9.7
Reflection shellResolution: 2.9→3.09 Å / Redundancy: 14.2 % / Rmerge(I) obs: 2.48 / Mean I/σ(I) obs: 1 / CC1/2: 0.51 / Rpim(I) all: 0.94 / Rrim(I) all: 2.56 / % possible all: 21

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
Cootmodel building
BUSTER2.10.3refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JEY

1jey


Resolution: 2.9→48.76 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.916 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.458
RfactorNum. reflection% reflectionSelection details
Rfree0.244 2605 5.04 %RANDOM
Rwork0.218 ---
obs0.22 51644 72.9 %-
Displacement parametersBiso max: 225.95 Å2 / Biso mean: 100.04 Å2 / Biso min: 28.61 Å2
Baniso -1Baniso -2Baniso -3
1--1.9913 Å20 Å23.0498 Å2
2--1.6561 Å20 Å2
3---0.3352 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 2.9→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16821 2133 0 20 18974
Biso mean---51.16 -
Num. residues----2190
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d6746SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2986HARMONIC5
X-RAY DIFFRACTIONt_it19574HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2530SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact20557SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d19574HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg26846HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.17
X-RAY DIFFRACTIONt_other_torsion18.24
LS refinement shellResolution: 2.9→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3179 34 5.53 %
Rwork0.3136 581 -
all0.3138 615 -
obs--11.8 %
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)
15.6133-0.56181.43430.2345-0.19721.097-0.07290.01630.62240.0191-0.0544-0.003-0.1224-0.12010.1273-0.0210.03480.0184-0.0317-0.15710.006438.9878-6.237153.2216
24.29110.8380.38970.43710.09531.1302-0.0576-0.51310.1009-0.0116-0.0061-0.0427-0.07710.09310.0637-0.03-0.00940.0543-0.342-0.0452-0.1068-6.1283-8.2204211.1613
36.41030.1556-1.77392.7085-0.32756.08820.01290.3805-0.2364-0.50590.05170.57180.67180.1087-0.06460.07460.0676-0.12080.28710.03920.039446.0657-18.3926137.5107
43.6443-0.7985-2.91912.7020.54357.5174-0.018-0.6442-0.24770.5680.0064-0.57910.653-0.21630.01170.1348-0.1739-0.10760.3231-0.00130.0985-13.8995-19.597227.2849
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* B|* F|* }A34 - 534
2X-RAY DIFFRACTION1{ A|* B|* F|* }B-16 - 542
3X-RAY DIFFRACTION1{ A|* B|* F|* }F293 - 299
4X-RAY DIFFRACTION2{ D|* E|* C|* }D32 - 534
5X-RAY DIFFRACTION2{ D|* E|* C|* }E-16 - 543
6X-RAY DIFFRACTION2{ D|* E|* C|* }C293 - 299
7X-RAY DIFFRACTION3{ H|* R|* }H1 - 21
8X-RAY DIFFRACTION3{ H|* R|* }R1 - 34
9X-RAY DIFFRACTION4{ K|* M|* }K1 - 21
10X-RAY DIFFRACTION4{ K|* M|* }M1 - 34

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