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- PDB-5w4g: Importin binding to NLS peptide of DNA polymerase lambda -

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Basic information

Entry
Database: PDB / ID: 5w4g
TitleImportin binding to NLS peptide of DNA polymerase lambda
Components
  • DNA polymerase lambda
  • Importin subunit alpha-1
KeywordsPROTEIN BINDING / importin / NLS / polymerase lambda / 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 / DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases ...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 / DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / cytoplasmic stress granule / protein import into nucleus / host cell / site of double-strand break / DNA-binding transcription factor binding / DNA replication / DNA-directed DNA polymerase / postsynaptic density / DNA-directed DNA polymerase activity / glutamatergic synapse / DNA binding / nucleoplasm / nucleus / metal ion binding / cytosol
Similarity search - Function
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 / Leucine-rich Repeat Variant ...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 / Leucine-rich Repeat Variant / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / DNA polymerase family X, beta-like / 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, thumb domain superfamily / DNA polymerase beta thumb / 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 polymerase lambda
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.038 Å
AuthorsPedersen, L.C. / London, R.E.
CitationJournal: To Be Published
Title: Structure of Importin with bound NLS from DNA polymerase lambda
Authors: Pedersen, L.C. / London, R. / Gabel, S.
History
DepositionJun 10, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 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

Downloads & links

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Assembly

Deposited unit
B: Importin subunit alpha-1
A: DNA polymerase lambda
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1327
Polymers58,6562
Non-polymers4765
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-42 kcal/mol
Surface area17410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.195, 89.747, 98.510
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 polymerase lambda / Pol Lambda / DNA polymerase beta-2 / Pol beta2 / DNA polymerase kappa


Mass: 3325.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.95 Å3/Da / Density % sol: 58.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M Bis Tris Propane 1.4 M Ammonium Sulfate

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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: Sep 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.038→50 Å / Num. obs: 41954 / % possible obs: 96.9 % / Redundancy: 5.4 % / Rsym value: 0.071 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.14 Å / Rsym value: 0.347

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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: 2.038→37.799 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 20.66
RfactorNum. reflection% reflection
Rfree0.1998 2090 4.99 %
Rwork0.1707 --
obs0.1721 41857 93.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.038→37.799 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3234 0 26 250 3510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043349
X-RAY DIFFRACTIONf_angle_d0.6894583
X-RAY DIFFRACTIONf_dihedral_angle_d13.1221183
X-RAY DIFFRACTIONf_chiral_restr0.043559
X-RAY DIFFRACTIONf_plane_restr0.004586
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0383-2.08570.363320.2685766X-RAY DIFFRACTION27
2.0857-2.13790.22371260.2252420X-RAY DIFFRACTION87
2.1379-2.19570.25991380.21072545X-RAY DIFFRACTION91
2.1957-2.26030.22191400.19392661X-RAY DIFFRACTION95
2.2603-2.33320.22071460.18472766X-RAY DIFFRACTION98
2.3332-2.41660.24471480.18812786X-RAY DIFFRACTION99
2.4166-2.51330.21181480.17882820X-RAY DIFFRACTION100
2.5133-2.62770.23631480.18232806X-RAY DIFFRACTION100
2.6277-2.76620.19551500.17152837X-RAY DIFFRACTION100
2.7662-2.93940.22421490.17462825X-RAY DIFFRACTION100
2.9394-3.16630.21331500.18392854X-RAY DIFFRACTION100
3.1663-3.48470.20511510.16782866X-RAY DIFFRACTION100
3.4847-3.98850.16481510.14832870X-RAY DIFFRACTION100
3.9885-5.02320.17791530.15052918X-RAY DIFFRACTION100
5.0232-37.80580.18771600.17223027X-RAY DIFFRACTION100

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