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- PDB-5w4f: Importin binding to pol Mu NLS peptide -

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Basic information

Entry
Database: PDB / ID: 5w4f
TitleImportin binding to pol Mu NLS peptide
Components
  • DNA-directed DNA/RNA polymerase mu
  • Importin subunit alpha-1
KeywordsPROTEIN BINDING / importin / NLS / Tdt / Nuclear Transport
Function / homology
Function and homology information


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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / Nonhomologous End-Joining (NHEJ) / cytoplasmic stress granule ...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 / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding / NLS-bearing protein import into nucleus / Nonhomologous End-Joining (NHEJ) / cytoplasmic stress granule / double-strand break repair via nonhomologous end joining / protein import into nucleus / host cell / DNA-binding transcription factor binding / DNA recombination / DNA-directed DNA polymerase / postsynaptic density / DNA-directed DNA polymerase activity / glutamatergic synapse / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / 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. ...DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / 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 / Leucine-rich Repeat Variant / DNA polymerase beta, palm domain / DNA polymerase beta palm / 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 family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / 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 / Mainly Alpha
Similarity search - Domain/homology
Importin subunit alpha-1 / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.984 Å
AuthorsPedersen, L.C. / London, R.E.
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 13, 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
A: DNA-directed DNA/RNA polymerase mu
D: DNA-directed DNA/RNA polymerase mu
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,5445
Polymers61,3593
Non-polymers1842
Water5,711317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: Two molecules of NLS polymerase mu peptides are binding one molecule of Importin
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint3 kcal/mol
Surface area17610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.005, 89.819, 99.541
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 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-directed DNA/RNA polymerase mu / Pol Mu / Terminal transferase


Mass: 3014.404 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: NLS peptide of DNA polymerase mu / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NP87, DNA-directed DNA polymerase
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 317 / 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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M HEPES 0.8 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: Jul 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 48426 / % possible obs: 97.4 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.9
Reflection shellResolution: 1.98→2.01 Å / Rmerge(I) obs: 0.38

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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: 1.984→40.936 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.14
RfactorNum. reflection% reflection
Rfree0.1988 2422 5.01 %
Rwork0.1695 --
obs0.1709 48351 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.984→40.936 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3255 0 12 317 3584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083414
X-RAY DIFFRACTIONf_angle_d1.0814669
X-RAY DIFFRACTIONf_dihedral_angle_d11.1382074
X-RAY DIFFRACTIONf_chiral_restr0.07565
X-RAY DIFFRACTIONf_plane_restr0.005602
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9837-2.02420.32271010.252008X-RAY DIFFRACTION73
2.0242-2.06820.25411300.21962362X-RAY DIFFRACTION87
2.0682-2.11640.29271400.20492617X-RAY DIFFRACTION95
2.1164-2.16930.24571410.18952690X-RAY DIFFRACTION99
2.1693-2.22790.21511450.18172749X-RAY DIFFRACTION100
2.2279-2.29350.19841390.17552733X-RAY DIFFRACTION100
2.2935-2.36750.22171500.17772767X-RAY DIFFRACTION100
2.3675-2.45210.23271450.17742741X-RAY DIFFRACTION100
2.4521-2.55030.23841490.18042778X-RAY DIFFRACTION100
2.5503-2.66630.21981470.18442749X-RAY DIFFRACTION100
2.6663-2.80690.22321430.17572774X-RAY DIFFRACTION100
2.8069-2.98270.20881460.18252773X-RAY DIFFRACTION100
2.9827-3.21290.21481480.18032772X-RAY DIFFRACTION100
3.2129-3.5360.2181450.17692807X-RAY DIFFRACTION100
3.536-4.04730.15931480.1462800X-RAY DIFFRACTION100
4.0473-5.09770.15431480.13962842X-RAY DIFFRACTION100
5.0977-40.94480.17471570.16592967X-RAY DIFFRACTION99

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