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- PDB-5w7x: Crystal Structure of FHA domain of human APLF in complex with XRC... -

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Basic information

Entry
Database: PDB / ID: 5w7x
TitleCrystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho 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 / positive regulation of DNA ligase activity / 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 / histone chaperone activity ...3' overhang single-stranded DNA endodeoxyribonuclease activity / oxidized DNA binding / positive regulation of DNA ligase activity / 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 / histone chaperone activity / poly-ADP-D-ribose binding / positive regulation of single strand break repair / positive regulation of DNA ligation / regulation of epithelial to mesenchymal transition / voluntary musculoskeletal movement / cerebellum morphogenesis / single strand break repair / replication-born double-strand break repair via sister chromatid exchange / HDR through MMEJ (alt-NHEJ) / response to hydroperoxide / DNA repair-dependent chromatin remodeling / Resolution of AP sites via the single-nucleotide replacement pathway / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / site of DNA damage / protein folding chaperone / protein localization to chromatin / DNA-(apurinic or apyrimidinic site) endonuclease activity / 3'-5' exonuclease activity / 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 / chromosome, telomeric region / Hydrolases; Acting on ester bonds / response to hypoxia / response to xenobiotic stimulus / DNA repair / nucleotide binding / DNA damage response / chromatin / nucleolus / enzyme binding / nucleoplasm / nucleus / metal ion binding / 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, a BRCA1 C-terminus 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, a BRCA1 C-terminus 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: 2.005 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,1398
Polymers52,1398
Non-polymers00
Water4,666259
1
D: Aprataxin and PNK-like factor
H: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)13,0352
Polymers13,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area840 Å2
ΔGint-4 kcal/mol
Surface area6100 Å2
MethodPISA
2
A: Aprataxin and PNK-like factor
E: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)13,0352
Polymers13,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-5 kcal/mol
Surface area6130 Å2
MethodPISA
3
B: Aprataxin and PNK-like factor
F: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)13,0352
Polymers13,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-5 kcal/mol
Surface area5940 Å2
MethodPISA
4
C: Aprataxin and PNK-like factor
G: DNA repair protein XRCC1


Theoretical massNumber of molelcules
Total (without water)13,0352
Polymers13,0352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-5 kcal/mol
Surface area6110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.119, 36.799, 98.284
Angle α, β, γ (deg.)90.00, 90.86, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 4 / 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: 1112.878 Da / Num. of mol.: 4 / Fragment: UNP residues 514-522 / Source method: obtained synthetically / Details: bisphosphopeptide of XRCC1 / Source: (synth.) Homo sapiens (human) / References: UniProt: P18887
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.005→25.497 Å / Num. obs: 28032 / % possible obs: 97.9 % / Redundancy: 4.8 % / Rpim(I) all: 0.031 / Rsym value: 0.065 / Net I/σ(I): 13.4
Reflection shellResolution: 2.005→2.05 Å / Redundancy: 2.4 % / Num. unique obs: 1098 / Rpim(I) all: 0.214 / Rsym value: 0.295 / % possible all: 75.3

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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: 5W7W

5w7w


Resolution: 2.005→25.497 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.24
RfactorNum. reflection% reflectionSelection details
Rfree0.2291 1390 4.97 %random
Rwork0.1922 ---
obs0.194 27941 96.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.005→25.497 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3347 0 0 259 3606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033462
X-RAY DIFFRACTIONf_angle_d0.5814722
X-RAY DIFFRACTIONf_dihedral_angle_d18.6011296
X-RAY DIFFRACTIONf_chiral_restr0.045514
X-RAY DIFFRACTIONf_plane_restr0.004610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0054-2.0770.28881000.2431926X-RAY DIFFRACTION71
2.077-2.16020.26951430.22012702X-RAY DIFFRACTION99
2.1602-2.25840.2391480.20242696X-RAY DIFFRACTION100
2.2584-2.37740.28971360.21612739X-RAY DIFFRACTION100
2.3774-2.52620.30331460.23312704X-RAY DIFFRACTION100
2.5262-2.72110.35231400.24542713X-RAY DIFFRACTION99
2.7211-2.99450.28051450.23932704X-RAY DIFFRACTION99
2.9945-3.42690.23231480.19662729X-RAY DIFFRACTION100
3.4269-4.31420.17611370.1572781X-RAY DIFFRACTION100
4.3142-25.49890.19111470.16862857X-RAY DIFFRACTION99

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