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- PDB-1ejy: MOUSE IMPORTIN ALPHA-NUCLEOPLASMIN NLS PEPTIDE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1ejy
TitleMOUSE IMPORTIN ALPHA-NUCLEOPLASMIN NLS PEPTIDE COMPLEX
Components
  • IMPORTIN ALPHA
  • NUCLEOPLASMIN NLS PEPTIDE
KeywordsHydrolase/Peptide / importin aplpha/karyopherin alpha / nuclear localization sequence (NLS) recognition / nucleoplasmin / PROTEIN BINDING / Hydrolase-Peptide complex
Function / homology
Function and homology information


sperm DNA decondensation / histone chaperone activity / 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 / importin-alpha family protein binding / NLS-dependent protein nuclear import complex / postsynapse to nucleus signaling pathway / nuclear import signal receptor activity / nuclear localization sequence binding ...sperm DNA decondensation / histone chaperone activity / 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 / importin-alpha family protein binding / 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 / nucleosome binding / positive regulation of DNA replication / cytoplasmic stress granule / protein import into nucleus / host cell / histone binding / DNA-binding transcription factor binding / postsynaptic density / chromatin remodeling / glutamatergic synapse / nucleolus / RNA binding / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / 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 ...Nucleoplasmin core domain / Nucleoplasmin core domain superfamily / Nucleoplasmin/nucleophosmin domain / Nucleoplasmin family / 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 / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Nucleoplasmin / Importin subunit alpha-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsFontes, M.R. / Teh, T. / Kobe, B.
Citation
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. / Teh, T. / Kobe, B.
#1: 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
DepositionMar 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
N: NUCLEOPLASMIN NLS PEPTIDE
I: IMPORTIN ALPHA


Theoretical massNumber of molelcules
Total (without water)51,6342
Polymers51,6342
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.901, 89.828, 99.903
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 NUCLEOPLASMIN NLS PEPTIDE


Mass: 1747.178 Da / Num. of mol.: 1
Fragment: NLS (NUCLEAR LOCALIZATION SIGNAL) BIPARTITE PEPTIDE, RESIDUES 155-170
Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of this peptide is naturally found in Xenopus laevis (African clawed frog).
References: UniProt: P05221
#2: Protein IMPORTIN ALPHA / KARYOPHERIN


Mass: 49886.633 Da / Num. of mol.: 1 / Fragment: NLS BINDING DOMAIN, RESIDUES 70-529
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / References: UniProt: P52293

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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: 3.43 Å3/Da / Density % sol: 64.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium citrate, Hepes, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.55 Msodium citrate11
2100 mMHEPES11
310 mMdithiothreitol11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Sep 9, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 121070 / Num. obs: 16370 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 68.3 Å2 / Rmerge(I) obs: 0.239 / Net I/σ(I): 7.2
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.962 / Num. unique all: 1598 / % possible all: 100
Reflection
*PLUS
Num. measured all: 121070
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 1598 / Mean I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.4refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.9→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1331801.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: protein_rep.param
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1585 9.8 %RANDOM (10%)
Rwork0.223 ---
all0.223 16102 --
obs0.223 16102 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.39 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 37.2 Å2
Baniso -1Baniso -2Baniso -3
1--3.76 Å20 Å20 Å2
2---4.39 Å20 Å2
3---8.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3366 0 0 0 3366
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_d19.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.791.5
X-RAY DIFFRACTIONc_mcangle_it1.422
X-RAY DIFFRACTIONc_scbond_it1.022
X-RAY DIFFRACTIONc_scangle_it1.692.5
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.355 151 9.5 %
Rwork0.345 1439 -
obs--100 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.355 / % reflection Rfree: 9.5 % / Rfactor Rwork: 0.345 / Rfactor obs: 0.345

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