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- PDB-6erf: Complex of APLF factor and Ku heterodimer bound to DNA -

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Basic information

Entry
Database: PDB / ID: 6erf
TitleComplex of APLF factor and Ku heterodimer bound to DNA
Components
  • (X-ray repair cross-complementing protein ...) x 2
  • Aprataxin and PNK-like factor
  • DNA (34-MER)
  • DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')
KeywordsDNA BINDING PROTEIN / DNA repair protein NHEJ
Function / homology
Function and homology information


ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / Ku70:Ku80 complex / poly-ADP-D-ribose binding / negative regulation of t-circle formation / histone chaperone activity / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex ...ADP-D-ribose modification-dependent protein binding / regulation of isotype switching / Ku70:Ku80 complex / poly-ADP-D-ribose binding / negative regulation of t-circle formation / histone chaperone activity / 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 / cellular response to X-ray / nonhomologous end joining complex / regulation of epithelial to mesenchymal transition / regulation of smooth muscle cell proliferation / single strand break repair / 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 / regulation of telomere maintenance / recombinational repair / U3 snoRNA binding / protein localization to chromosome, telomeric region / cellular response to fatty acid / cellular hyperosmotic salinity response / positive regulation of neurogenesis / telomeric DNA binding / 2-LTR circle formation / hematopoietic stem cell proliferation / DNA repair-dependent chromatin remodeling / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / ATP-dependent activity, acting on DNA / positive regulation of protein kinase activity / hematopoietic stem cell differentiation / telomere maintenance via telomerase / DNA helicase activity / protein localization to chromatin / neurogenesis / 3'-5' exonuclease activity / DNA-(apurinic or apyrimidinic site) endonuclease activity / embryo implantation / telomere maintenance / protein folding chaperone / activation of innate immune response / cyclin binding / cellular response to leukemia inhibitory factor / enzyme activator activity / DNA endonuclease activity / Nonhomologous End-Joining (NHEJ) / small-subunit processome / cellular response to gamma radiation / protein-DNA complex / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / double-strand break repair via nonhomologous end joining / double-strand break repair / site of double-strand break / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA recombination / transcription regulator complex / histone binding / ficolin-1-rich granule lumen / damaged DNA binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / transcription cis-regulatory region binding / response to xenobiotic stimulus / ribonucleoprotein complex / innate immune response / DNA repair / nucleotide binding / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / Neutrophil degranulation / protein-containing complex binding / positive regulation of DNA-templated transcription / nucleolus / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / DNA binding / RNA binding / extracellular region / zinc ion binding / 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 / Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / Ku70; Chain: A; domain 4 / Ku70; Chain: A; domain 4 - #10 / PBZ domain / PNK, FHA domain ...Ku70, bridge and pillars / Ku70, bridge and pillars / Ku70; Chain: A; Domain 2 - #10 / Ku70; Chain: A; Domain 2 / Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / Ku70; Chain: A; domain 4 / Ku70; Chain: A; domain 4 - #10 / PBZ domain / PNK, FHA domain / FHA domain / 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 beta-barrel domain / Ku70/Ku80 N-terminal alpha/beta 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 / SMAD/FHA domain superfamily / 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 / Aprataxin and PNK-like factor
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.01 Å
AuthorsNemoz, C. / Legrand, P. / Ropars, V. / Charbonnier, J.B.
Funding support France, 3items
OrganizationGrant numberCountry
INCAPLBIO 2012-280 France
French National Research AgencyANR-12-SVSE8-012 France
ARCSLS220120605310 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 1.2Jun 23, 2021Group: Database references / Refinement description / Category: citation / software / Item: _citation.journal_abbrev / _software.classification
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: X-ray repair cross-complementing protein 6
B: X-ray repair cross-complementing protein 5
C: X-ray repair cross-complementing protein 6
D: X-ray repair cross-complementing protein 5
E: X-ray repair cross-complementing protein 6
F: X-ray repair cross-complementing protein 5
G: X-ray repair cross-complementing protein 6
H: X-ray repair cross-complementing protein 5
I: DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')
J: DNA (34-MER)
K: DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')
L: DNA (34-MER)
M: DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')
N: DNA (34-MER)
O: DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')
P: DNA (34-MER)
Q: Aprataxin and PNK-like factor
R: Aprataxin and PNK-like factor
S: Aprataxin and PNK-like factor
T: Aprataxin and PNK-like factor


Theoretical massNumber of molelcules
Total (without water)588,17620
Polymers588,17620
Non-polymers00
Water1448
1
A: X-ray repair cross-complementing protein 6
B: X-ray repair cross-complementing protein 5
I: DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')
J: DNA (34-MER)
Q: Aprataxin and PNK-like factor


Theoretical massNumber of molelcules
Total (without water)147,0445
Polymers147,0445
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: X-ray repair cross-complementing protein 6
D: X-ray repair cross-complementing protein 5
K: DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')
L: DNA (34-MER)
R: Aprataxin and PNK-like factor


Theoretical massNumber of molelcules
Total (without water)147,0445
Polymers147,0445
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: X-ray repair cross-complementing protein 6
F: X-ray repair cross-complementing protein 5
M: DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')
N: DNA (34-MER)
S: Aprataxin and PNK-like factor


Theoretical massNumber of molelcules
Total (without water)147,0445
Polymers147,0445
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: X-ray repair cross-complementing protein 6
H: X-ray repair cross-complementing protein 5
O: DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')
P: DNA (34-MER)
T: Aprataxin and PNK-like factor


Theoretical massNumber of molelcules
Total (without water)147,0445
Polymers147,0445
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.920, 140.860, 150.310
Angle α, β, γ (deg.)68.640, 80.850, 81.230
Int Tables number1
Space group name H-MP1

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Components

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X-ray repair cross-complementing protein ... , 2 types, 8 molecules ACEGBDFH

#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.: 4
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.: 4
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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DNA chain , 2 types, 8 molecules IKMOJLNP

#3: DNA chain
DNA (5'-D(*GP*TP*TP*TP*TP*TP*AP*GP*TP*TP*TP*AP*TP*TP*GP*GP*GP*CP*GP*CP*G)-3')


Mass: 6506.188 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain
DNA (34-MER)


Mass: 10325.685 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein/peptide / Non-polymers , 2 types, 12 molecules QRST

#5: Protein/peptide
Aprataxin and PNK-like factor / Apurinic-apyrimidinic endonuclease APLF / PNK and APTX-like FHA domain-containing protein / XRCC1- ...Apurinic-apyrimidinic endonuclease APLF / PNK and APTX-like FHA domain-containing protein / XRCC1-interacting protein 1


Mass: 2225.740 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q8IW19, DNA-(apurinic or apyrimidinic site) lyase
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.26 Å3/Da / Density % sol: 62.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.01→49.47 Å / Num. obs: 90993 / % possible obs: 61.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 123 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.051 / Rrim(I) all: 0.072 / Net I/σ(I): 11.8
Reflection shellResolution: 3.01→3.28 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 1.3 / CC1/2: 0.6 / Rpim(I) all: 0.66 / Rrim(I) all: 0.93 / % possible all: 14.3

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1jey


Resolution: 3.01→49.47 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.907 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.474
RfactorNum. reflection% reflectionSelection details
Rfree0.227 4537 4.99 %RANDOM
Rwork0.209 ---
obs0.21 90993 61.9 %-
Displacement parametersBiso max: 263.38 Å2 / Biso mean: 121.75 Å2 / Biso min: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1--1.4816 Å2-1.8203 Å20.7494 Å2
2---0.6188 Å23.2933 Å2
3---2.1003 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 3.01→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms33225 2178 0 7 35410
Biso mean---59.78 -
Num. residues----4233
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d12833SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes5768HARMONIC5
X-RAY DIFFRACTIONt_it36316HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion4718SEMIHARMONIC5
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_contact37519SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d36316HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg49413HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion1.84
X-RAY DIFFRACTIONt_other_torsion19.81
LS refinement shellResolution: 3.01→3.09 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.4683 3 -
all0.4683 --
obs--0.04 %
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)
11.03361.26860.36664.59622.72171.9923-0.0161-0.32090.23030.7463-0.53980.7930.4653-0.2720.5559-0.1627-0.02830.09110.05630.0522-0.096148.0479-9.5326141.2243
23.34280.9986-1.76821.1539-0.03431.3647-0.09280.1676-0.2614-0.24670.0228-0.4567-0.1606-0.1580.07-0.0243-0.0053-0.0573-0.14950.098-0.0567119.951550.9509138.2239
31.5530.813-1.09371.13790.09391.4504-0.01440.07060.0074-0.0258-0.10410.3752-0.028-0.04090.1186-0.23910.0452-0.1549-0.15830.103-0.0041127.5088-5.479880.0481
40.80011.28270.22164.33452.67882.5568-0.17170.1964-0.0887-0.68040.3975-0.3164-0.22650.0787-0.2259-0.10860.02360.07-0.10640.0478-0.044287.665864.806164.8943
52.7194-0.6365-1.77935.1678-2.14476.16840.0285-0.0687-0.24960.10510.0496-0.04080.26260.0424-0.07810.4170.12230.00540.25390.02260.1665155.9783-15.4591154.6267
68.20091.3511.93392.73092.51496.99870.00170.13570.033-0.1930.04220.28460.0748-0.3097-0.04380.22890.04160.0170.40880.11960.2359109.746252.0686123.5518
73.1353-3.6195-2.53277.2793-0.53755.53650.01710.29280.2162-0.2487-0.1206-0.057-0.19330.02440.10350.1785-0.0648-0.13550.36550.16790.3696118.51537.269473.1861
86.1292-1.6611-1.35544.85622.55091.6707-0.0161-0.17780.05050.2199-0.0029-0.2363-0.01730.23760.0190.35040.0750.00020.1438-0.08540.224999.49356.303871.5254
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* B|* Q|* }A35 - 535
2X-RAY DIFFRACTION1{ A|* B|* Q|* }B6 - 542
3X-RAY DIFFRACTION1{ A|* B|* Q|* }Q180 - 191
4X-RAY DIFFRACTION2{ C|* D|* R|* }C35 - 538
5X-RAY DIFFRACTION2{ C|* D|* R|* }D6 - 542
6X-RAY DIFFRACTION2{ C|* D|* R|* }R179 - 191
7X-RAY DIFFRACTION3{ E|* F|* S|* }E35 - 535
8X-RAY DIFFRACTION3{ E|* F|* S|* }F6 - 542
9X-RAY DIFFRACTION3{ E|* F|* S|* }S180 - 191
10X-RAY DIFFRACTION4{ G|* H|* T|* }G35 - 534
11X-RAY DIFFRACTION4{ G|* H|* T|* }H6 - 542
12X-RAY DIFFRACTION4{ G|* H|* T|* }T180 - 191
13X-RAY DIFFRACTION5{ I|* J|* }I2 - 15
14X-RAY DIFFRACTION5{ I|* J|* }J22 - 33
15X-RAY DIFFRACTION6{ K|* L|* }K4 - 16
16X-RAY DIFFRACTION6{ K|* L|* }L21 - 30
17X-RAY DIFFRACTION7{ M|* N|* }M4 - 16
18X-RAY DIFFRACTION7{ M|* N|* }N20 - 33
19X-RAY DIFFRACTION8{ O|* P|* }O2 - 15
20X-RAY DIFFRACTION8{ O|* P|* }P19 - 34

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