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- PDB-1pjn: Mouse Importin alpha-bipartite NLS N1N2 from Xenopus laevis phosp... -

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Basic information

Entry
Database: PDB / ID: 1pjn
TitleMouse Importin alpha-bipartite NLS N1N2 from Xenopus laevis phosphoprotein Complex
Components
  • Histone-binding protein N1/N2
  • Importin alpha-2 subunit
KeywordsPROTEIN TRANSPORT / IMPORTIN ALPHA/KARYOPHERIN ALPHA / NUCLEAR LOCALIZATION SEQUENCE (NLS) RECOGNITION / BIPARTITE NLS / Xenopus laevis N1N2 phosphoprotein
Function / homology
Function and homology information


CENP-A containing chromatin assembly / 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 / DNA replication-dependent chromatin assembly / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule ...CENP-A containing chromatin assembly / 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 / DNA replication-dependent chromatin assembly / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / cytoplasmic stress granule / protein import into nucleus / host cell / histone binding / DNA-binding transcription factor binding / postsynaptic density / glutamatergic synapse / nucleoplasm / cytosol
Similarity search - Function
Tetratricopeptide, SHNi-TPR domain / : / SHNi-TPR / 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. ...Tetratricopeptide, SHNi-TPR domain / : / SHNi-TPR / 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 / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Armadillo-like helical / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Histone-binding protein N1/N2 / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsFontes, M.R.M. / Teh, T. / Jans, D. / Brinkworth, R.I. / Kobe, B.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Structural basis for the specificity of bipartite nuclear localization sequence binding by importin-alpha
Authors: Fontes, M.R.M. / Teh, T. / Jans, D. / Brinkworth, R.I. / Kobe, B.
#1: Journal: J.Mol.Biol. / Year: 2000
Title: Structural basis of recognition of monopartite and bipartite nuclear localization sequences by mammalian importin-alpha
Authors: Fontes, M.R.M. / Teh, T. / Kobe, B.
#2: Journal: J.Biol.Chem. / Year: 2001
Title: Biophysical Characterization of Interactions Involving Impostin-alpha during Nuclear Import
Authors: Catimel, B. / Teh, T. / Fontes, M.R.M. / Jennings, I.G. / Jans, D. / Howlett, G.J. / Nice, E.C. / Kobe, B.
#3: Journal: Nat.Struct.Biol. / Year: 1999
Title: Autoinhibition by an internal nuclear localization signal reveled by the crystal structure of mammalian importin alpha
Authors: Kobe, B.
History
DepositionJun 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histone-binding protein N1/N2
B: Importin alpha-2 subunit


Theoretical massNumber of molelcules
Total (without water)52,3692
Polymers52,3692
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.920, 89.769, 101.042
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 Histone-binding protein N1/N2


Mass: 2481.932 Da / Num. of mol.: 1
Fragment: NLS (nuclear localization signal) bipartite peptide
Mutation: Q555G / Source method: obtained synthetically
Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE IS NATURALLY FOUND IN Xenopus laevis N1N2 phosphoprotein
References: UniProt: P52293, UniProt: P06180*PLUS
#2: Protein Importin alpha-2 subunit / Karyopherin alpha-2 subunit


Mass: 49886.633 Da / Num. of mol.: 1 / Fragment: NLS binding domain (70-529)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: KPNA2 OR RCH1 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / References: UniProt: P06180, UniProt: P52293*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.42 Å3/Da / Density % sol: 63.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Sodium Citrate, DTT, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.7 mg/mlprotein1drop
20.6 Msodium citrate1reservoirpH6.0
310 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 2000 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→99 Å / Num. all: 25538 / Num. obs: 25538 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 58.2 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 15.7
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.515 / Mean I/σ(I) obs: 1.8 / % possible all: 94.6
Reflection
*PLUS
Num. measured all: 211968
Reflection shell
*PLUS
% possible obs: 94.6 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY: 1ial

1ial


Resolution: 2.5→29.64 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1169 4.8 %RANDOM
Rwork0.209 ---
obs0.209 24340 95.5 %-
all-24340 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.0074 Å2 / ksol: 0.348618 e/Å3
Displacement parametersBiso mean: 51.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2---7.53 Å20 Å2
3---8.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 0 123 3525
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it1.912
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.316 205 5.1 %
Rwork0.296 3839 -
obs-4210 96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 30 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.93
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.326 / Rfactor Rwork: 0.302

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