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- PDB-5w4e: Importin binding to Tdt NLS peptide -

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Basic information

Entry
Database: PDB / ID: 5w4e
TitleImportin binding to Tdt NLS peptide
Components
  • Importin subunit alpha-1,Importin subunit alpha-1
  • human DNA repair polymerase Tdt
KeywordsPROTEIN BINDING / importin / NLS / Tdt / Nuclear Transport
Function / homology
Function and homology information


DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / arginine metabolic process / DNA modification / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / arginase / arginase activity / positive regulation of viral life cycle / urea cycle ...DNA nucleotidylexotransferase / DNA nucleotidylexotransferase activity / arginine metabolic process / DNA modification / Sensing of DNA Double Strand Breaks / entry of viral genome into host nucleus through nuclear pore complex via importin / arginase / arginase activity / positive regulation of viral life cycle / urea cycle / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / DNA metabolic process / NLS-bearing protein import into nucleus / response to ATP / host cell / euchromatin / nuclear matrix / cytoplasmic stress granule / double-strand break repair via nonhomologous end joining / protein import into nucleus / DNA-binding transcription factor binding / postsynaptic density / DNA-directed DNA polymerase activity / glutamatergic synapse / DNA binding / nucleoplasm / metal ion binding / nucleus / cytosol
Similarity search - Function
DNA nucleotidylexotransferase (TdT) / Arginase / Polymerase, nucleotidyl transferase domain / Ureohydrolase, manganese-binding site / Arginase family signature. / Nucleotidyltransferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Ureohydrolase / Arginase family / Arginase family profile. ...DNA nucleotidylexotransferase (TdT) / Arginase / Polymerase, nucleotidyl transferase domain / Ureohydrolase, manganese-binding site / Arginase family signature. / Nucleotidyltransferase domain / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Ureohydrolase / Arginase family / Arginase family profile. / 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 / Ureohydrolase domain superfamily / breast cancer carboxy-terminal domain / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Winged helix-like DNA-binding domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Arginase / DNA nucleotidylexotransferase / Importin subunit alpha-1
Similarity search - Component
Biological speciesGlaciozyma antarctica (fungus)
Mus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsPedersen, L.C. / London, R.
CitationJournal: Traffic / Year: 2018
Title: Variations in nuclear localization strategies among pol X family enzymes.
Authors: Kirby, T.W. / Pedersen, L.C. / Gabel, S.A. / Gassman, N.R. / London, R.E.
History
DepositionJun 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
B: Importin subunit alpha-1,Importin subunit alpha-1
A: human DNA repair polymerase Tdt
D: human DNA repair polymerase Tdt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2836
Polymers59,0073
Non-polymers2763
Water4,918273
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-3 kcal/mol
Surface area17570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.683, 89.493, 100.296
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 Importin subunit alpha-1,Importin subunit alpha-1 / / Importin alpha P1 / Importin alpha P1 / Karyopherin subunit alpha-2 / Pendulin / Pore targeting ...Importin alpha P1 / 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.) Glaciozyma antarctica (fungus), (gene. exp.) Mus musculus (house mouse)
Gene: Kpna2, Rch1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52293, UniProt: A0A2R2JFW7*PLUS
#2: Protein/peptide human DNA repair polymerase Tdt


Mass: 1838.166 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: NLS peptide for human DNA repair polymerase Tdt / Source: (synth.) Homo sapiens (human) / References: UniProt: P04053*PLUS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / 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: 3.09 Å3/Da / Density % sol: 60.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES 0.7 M Sodium Citrate

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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: Aug 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 36690 / % possible obs: 97.3 % / Redundancy: 6.7 % / Rsym value: 0.071 / Net I/σ(I): 10.8
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3.3 / Rsym value: 0.328 / % possible all: 76.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5E6Q

5e6q


Resolution: 2.18→40.864 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.45 / Phase error: 19.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1924 1835 5.02 %random
Rwork0.1653 ---
obs0.1667 36547 97.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.18→40.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3262 0 18 273 3553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013362
X-RAY DIFFRACTIONf_angle_d1.1324588
X-RAY DIFFRACTIONf_dihedral_angle_d11.8162036
X-RAY DIFFRACTIONf_chiral_restr0.066558
X-RAY DIFFRACTIONf_plane_restr0.006589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.2390.2371080.2112093X-RAY DIFFRACTION77
2.239-2.30490.25371340.18822396X-RAY DIFFRACTION89
2.3049-2.37920.25411450.1852622X-RAY DIFFRACTION97
2.3792-2.46430.21211250.17732718X-RAY DIFFRACTION99
2.4643-2.56290.24631560.17782703X-RAY DIFFRACTION100
2.5629-2.67950.22211420.17312715X-RAY DIFFRACTION100
2.6795-2.82080.19191420.16612736X-RAY DIFFRACTION100
2.8208-2.99750.20381470.1742735X-RAY DIFFRACTION100
2.9975-3.22880.22811450.18072739X-RAY DIFFRACTION100
3.2288-3.55360.19981460.17142763X-RAY DIFFRACTION100
3.5536-4.06740.171420.14742764X-RAY DIFFRACTION100
4.0674-5.12290.15341490.1382806X-RAY DIFFRACTION100
5.1229-40.87120.17111540.17132922X-RAY DIFFRACTION100

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