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- PDB-5ekg: Crystallization and X-ray Diffraction Data Collection of Importin... -

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Basic information

Entry
Database: PDB / ID: 5ekg
TitleCrystallization and X-ray Diffraction Data Collection of Importin-alpha from Mus musculus Complexed with a XPG NLS Peptide, fragment 2
Components
  • Importin subunit alpha-1
  • XPG2 peptide
KeywordsPROTEIN BINDING / Importin alpha / nuclear import pathway / nuclear localization sequence (NLS) / DNA repair proteins / nucleotide excision repair / XPG protein
Function / homology
Function and homology information


nucleotide-excision repair complex / base-excision repair, AP site formation / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / bubble DNA binding / regulation of catalytic activity / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / host cell ...nucleotide-excision repair complex / base-excision repair, AP site formation / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / bubble DNA binding / regulation of catalytic activity / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / host cell / response to UV-C / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / RNA polymerase II complex binding / enzyme activator activity / transcription-coupled nucleotide-excision repair / response to UV / DNA endonuclease activity / nucleotide-excision repair / double-strand break repair via homologous recombination / Dual Incision in GG-NER / Formation of Incision Complex in GG-NER / cytoplasmic stress granule / Dual incision in TC-NER / protein import into nucleus / histone deacetylase binding / single-stranded DNA binding / chromosome / double-stranded DNA binding / endonuclease activity / nuclear membrane / DNA-binding transcription factor binding / postsynaptic density / damaged DNA binding / Hydrolases; Acting on ester bonds / glutamatergic synapse / protein-containing complex binding / negative regulation of apoptotic process / protein homodimerization activity / protein-containing complex / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
XPG/Rad2 endonuclease, eukaryotes / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...XPG/Rad2 endonuclease, eukaryotes / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / 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. / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / PIN-like domain superfamily / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
DNA excision repair protein ERCC-5 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 Å
AuthorsBarros, A.C. / Takeda, A.A.S. / Fontes, M.R.M.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Structural and Calorimetric Studies Demonstrate that Xeroderma Pigmentosum Type G (XPG) Can Be Imported to the Nucleus by a Classical Nuclear Import Pathway via a Monopartite NLS Sequence.
Authors: Barros, A.C. / Takeda, A.A. / Dreyer, T.R. / Velazquez-Campoy, A. / Kobe, B. / Fontes, M.R.
History
DepositionNov 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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: XPG2 peptide
C: XPG2 peptide
A: Importin subunit alpha-1


Theoretical massNumber of molelcules
Total (without water)60,1513
Polymers60,1513
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint2 kcal/mol
Surface area17350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.492, 90.842, 100.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide XPG2 peptide


Mass: 2410.018 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P28715*PLUS
#2: 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 / Fragment: UNP residues 70-529
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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.6-0.7 M sodium citrate, 10 mM DTT / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 17937 / % possible obs: 99.3 % / Redundancy: 4.4 % / Net I/σ(I): 6.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 2.8→33.933 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2281 914 5.1 %
Rwork0.1874 --
obs0.1896 17937 98.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→33.933 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 0 0 3165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013220
X-RAY DIFFRACTIONf_angle_d1.2824411
X-RAY DIFFRACTIONf_dihedral_angle_d14.0581104
X-RAY DIFFRACTIONf_chiral_restr0.045556
X-RAY DIFFRACTIONf_plane_restr0.006561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.94950.3451130.28022252X-RAY DIFFRACTION93
2.9495-3.13420.3071510.26632411X-RAY DIFFRACTION99
3.1342-3.3760.29141220.24312427X-RAY DIFFRACTION99
3.376-3.71530.2481240.20722447X-RAY DIFFRACTION99
3.7153-4.25210.21731260.17122470X-RAY DIFFRACTION99
4.2521-5.35380.20891420.15942491X-RAY DIFFRACTION100
5.3538-33.9350.19361360.16732525X-RAY DIFFRACTION96

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