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- PDB-5w7y: Crystal Structure of FHA domain of human APLF in complex with XRC... -

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Basic information

Entry
Database: PDB / ID: 5w7y
TitleCrystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated mutated peptide
Components
  • Aprataxin and PNK-like factor
  • DNA repair protein XRCC1
KeywordsPROTEIN BINDING / scaffold protein / DNA repair / NHEJ
Function / homology
Function and homology information


3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / regulation of isotype switching / poly-ADP-D-ribose binding / histone chaperone activity ...3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / telomeric DNA-containing double minutes formation / ERCC4-ERCC1 complex / negative regulation of protection from non-homologous end joining at telomere / ADP-D-ribose modification-dependent protein binding / negative regulation of protein ADP-ribosylation / regulation of isotype switching / poly-ADP-D-ribose binding / histone chaperone activity / regulation of base-excision repair / regulation of epithelial to mesenchymal transition / single strand break repair / HDR through MMEJ (alt-NHEJ) / response to hydroperoxide / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / DNA repair-dependent chromatin remodeling / site of DNA damage / protein localization to chromatin / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / protein folding chaperone / embryo implantation / Gap-filling DNA repair synthesis and ligation in GG-NER / DNA endonuclease activity / hippocampus development / base-excision repair / double-strand break repair via nonhomologous end joining / Gap-filling DNA repair synthesis and ligation in TC-NER / double-strand break repair / site of double-strand break / histone binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / DNA repair / nucleotide binding / DNA damage response / chromatin / nucleolus / enzyme binding / zinc ion binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / PBZ domain / PNK, FHA domain / FHA domain / Tumour Suppressor Smad4 - #20 / BRCT domain ...Aprataxin and PNK-like factor, PBZ domain / Aprataxin and PNK-like factor / DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / PBZ domain / PNK, FHA domain / FHA domain / Tumour Suppressor Smad4 - #20 / BRCT domain / Tumour Suppressor Smad4 / SMAD/FHA domain superfamily / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Galactose-binding-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA repair protein XRCC1 / Aprataxin and PNK-like factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsPedersen, L.C. / Kim, K. / London, R.E.
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Characterization of the APLF FHA-XRCC1 phosphopeptide interaction and its structural and functional implications.
Authors: Kim, K. / Pedersen, L.C. / Kirby, T.W. / DeRose, E.F. / London, R.E.
History
DepositionJun 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aprataxin and PNK-like factor
D: DNA repair protein XRCC1
B: Aprataxin and PNK-like factor
C: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)25,7654
Polymers25,7654
Non-polymers00
Water2,252125
1
A: Aprataxin and PNK-like factor
D: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)12,8832
Polymers12,8832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-4 kcal/mol
Surface area6040 Å2
MethodPISA
2
B: Aprataxin and PNK-like factor
C: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)12,8832
Polymers12,8832
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-4 kcal/mol
Surface area6000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.799, 31.072, 118.908
Angle α, β, γ (deg.)90.00, 97.84, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-242-

HOH

21B-248-

HOH

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Components

#1: Protein 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: 11921.815 Da / Num. of mol.: 2 / Fragment: UNP residues 1-105
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APLF, C2orf13, PALF, XIP1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IW19, DNA-(apurinic or apyrimidinic site) lyase
#2: Protein/peptide DNA repair protein XRCC1 / X-ray repair cross-complementing protein 1


Mass: 960.833 Da / Num. of mol.: 2 / Fragment: UNP residues 514-521 / Mutation: S518E / Source method: obtained synthetically / Details: XRCC1 S518E mutation pT peptide / Source: (synth.) Homo sapiens (human) / References: UniProt: P18887
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.95 Å3/Da / Density % sol: 36.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.6mM APLF 0.6mM XRCC1 peptide 0.1M Tris 30% PEG 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.1→29.449 Å / Num. obs: 11773 / % possible obs: 92.3 % / Redundancy: 2.4 % / Rpim(I) all: 0.23 / Rsym value: 0.112 / Net I/σ(I): 7.9
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 2.7 / Num. unique obs: 486 / Rpim(I) all: 0.23 / Rsym value: 0.316 / % possible all: 87.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W7X

5w7x


Resolution: 2.1→29.449 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 26.05
RfactorNum. reflection% reflectionSelection details
Rfree0.2373 582 4.94 %random
Rwork0.2026 ---
obs0.2043 11771 98.3 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→29.449 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1690 0 0 125 1815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041744
X-RAY DIFFRACTIONf_angle_d0.6732374
X-RAY DIFFRACTIONf_dihedral_angle_d14.8121044
X-RAY DIFFRACTIONf_chiral_restr0.045261
X-RAY DIFFRACTIONf_plane_restr0.005308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0951-2.30580.29681350.24022594X-RAY DIFFRACTION93
2.3058-2.63930.35861440.25182840X-RAY DIFFRACTION100
2.6393-3.32450.27211500.22382817X-RAY DIFFRACTION100
3.3245-29.45190.17751530.16722938X-RAY DIFFRACTION100

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