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- PDB-5e6q: Importin alpha binding to XRCC1 NLS peptide -

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Basic information

Entry
Database: PDB / ID: 5e6q
TitleImportin alpha binding to XRCC1 NLS peptide
Components
  • DNA repair protein XRCC1 NLS peptide
  • Importin subunit alpha-1
KeywordsPROTEIN BINDING / XRCC1 / Importin / NLS / bipartite
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 / poly-ADP-D-ribose binding / positive regulation of single strand break repair ...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 / poly-ADP-D-ribose binding / positive regulation of single strand break repair / Sensing of DNA Double Strand Breaks / voluntary musculoskeletal movement / cerebellum morphogenesis / single strand break repair / replication-born double-strand break repair via sister chromatid exchange / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NLS-dependent protein nuclear import complex / HDR through MMEJ (alt-NHEJ) / postsynapse to nucleus signaling pathway / response to hydroperoxide / nuclear import signal receptor activity / nuclear localization sequence binding / Resolution of AP sites via the single-nucleotide replacement pathway / NLS-bearing protein import into nucleus / APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway / site of DNA damage / Gap-filling DNA repair synthesis and ligation in GG-NER / : / hippocampus development / base-excision repair / cytoplasmic stress granule / double-strand break repair via nonhomologous end joining / Gap-filling DNA repair synthesis and ligation in TC-NER / protein import into nucleus / host cell / DNA-binding transcription factor binding / chromosome, telomeric region / postsynaptic density / response to hypoxia / response to xenobiotic stimulus / glutamatergic synapse / chromatin / nucleolus / enzyme binding / nucleoplasm / nucleus / cytosol
Similarity search - Function
DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / BRCT domain, a BRCA1 C-terminus domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain ...DNA-repair protein Xrcc1, N-terminal / XRCC1, first (central) BRCT domain / XRCC1 N terminal domain / BRCT domain, a BRCA1 C-terminus domain / Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / BRCA1 C Terminus (BRCT) domain / Leucine-rich Repeat Variant / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Galactose-binding-like domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
DNA repair protein XRCC1 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.305 Å
AuthorsPedersen, L.C. / Kirby, T.W. / Gassman, N.R. / Smith, C.E. / Gabel, S.A. / Sobhany, M. / Wilson, S.H. / London, R.E.
CitationJournal: Sci Rep / Year: 2015
Title: Nuclear Localization of the DNA Repair Scaffold XRCC1: Uncovering the Functional Role of a Bipartite NLS.
Authors: Kirby, T.W. / Gassman, N.R. / Smith, C.E. / Pedersen, L.C. / Gabel, S.A. / Sobhany, M. / Wilson, S.H. / London, R.E.
History
DepositionOct 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Importin subunit alpha-1
A: DNA repair protein XRCC1 NLS peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6056
Polymers59,3462
Non-polymers2594
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-23 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.668, 90.112, 100.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 2 molecules BA

#1: Protein Importin subunit alpha-1 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit ...Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting complex 58 kDa subunit / PTAC58 / RAG cohort protein 1 / SRP1-alpha


Mass: 55330.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293
#2: Protein/peptide DNA repair protein XRCC1 NLS peptide / X-ray repair cross-complementing protein 1


Mass: 4015.741 Da / Num. of mol.: 1 / Fragment: UNP residues 241-276 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P18887

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Non-polymers , 4 types, 232 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 3.01 Å3/Da / Density % sol: 59.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.5M Ammonium sulfate, 0.1M bis-tris propane

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 31129 / % possible obs: 96.6 % / Redundancy: 5.4 % / Net I/σ(I): 9.6

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UKY

3uky


Resolution: 2.305→42.407 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 2852 5.02 %Random selection
Rwork0.1735 ---
obs0.1753 31075 93.13 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.305→42.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 0 13 228 3504
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023379
X-RAY DIFFRACTIONf_angle_d0.684620
X-RAY DIFFRACTIONf_dihedral_angle_d10.6831214
X-RAY DIFFRACTIONf_chiral_restr0.046562
X-RAY DIFFRACTIONf_plane_restr0.004594
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3047-2.34440.29561020.24141999X-RAY DIFFRACTION70
2.3444-2.3870.32411310.25342261X-RAY DIFFRACTION78
2.387-2.43290.34861330.23552473X-RAY DIFFRACTION86
2.4329-2.48260.26591310.22222624X-RAY DIFFRACTION90
2.4826-2.53660.2421480.21862697X-RAY DIFFRACTION93
2.5366-2.59560.30371470.21782808X-RAY DIFFRACTION96
2.5956-2.66050.29211590.21072804X-RAY DIFFRACTION96
2.6605-2.73240.24651440.19982798X-RAY DIFFRACTION97
2.7324-2.81280.22631600.19452774X-RAY DIFFRACTION97
2.8128-2.90350.25271380.19392850X-RAY DIFFRACTION97
2.9035-3.00730.27381500.18852845X-RAY DIFFRACTION97
3.0073-3.12770.25761480.19252814X-RAY DIFFRACTION97
3.1277-3.26990.20671480.18752788X-RAY DIFFRACTION97
3.2699-3.44230.26621350.18012812X-RAY DIFFRACTION97
3.4423-3.65780.19231630.16082781X-RAY DIFFRACTION97
3.6578-3.94010.181450.14292785X-RAY DIFFRACTION96
3.9401-4.33620.16121460.13372801X-RAY DIFFRACTION96
4.3362-4.96280.15331420.13912754X-RAY DIFFRACTION96
4.9628-6.24950.20531410.18332783X-RAY DIFFRACTION96
6.2495-42.41460.15341410.16242733X-RAY DIFFRACTION94

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