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- PDB-1ee5: YEAST KARYOPHERIN (IMPORTIN) ALPHA IN A COMPLEX WITH A NUCLEOPLAS... -

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Basic information

Entry
Database: PDB / ID: 1ee5
TitleYEAST KARYOPHERIN (IMPORTIN) ALPHA IN A COMPLEX WITH A NUCLEOPLASMIN NLS PEPTIDE
Components
  • KARYOPHERIN ALPHA
  • NUCLEOPLASMIN
KeywordsTRANSPORT PROTEIN / Armadillo repeat
Function / homology
Function and homology information


sperm DNA decondensation / proteasome localization / importin-alpha family protein binding / histone chaperone activity / import into nucleus / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / protein targeting to membrane / nuclear import signal receptor activity ...sperm DNA decondensation / proteasome localization / importin-alpha family protein binding / histone chaperone activity / import into nucleus / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / protein targeting to membrane / nuclear import signal receptor activity / nucleosome binding / positive regulation of DNA replication / protein import into nucleus / disordered domain specific binding / nuclear envelope / histone binding / chromatin remodeling / chromatin binding / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / protein-containing complex / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Xenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsConti, E.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystallographic analysis of the specific yet versatile recognition of distinct nuclear localization signals by karyopherin alpha.
Authors: Conti, E. / Kuriyan, J.
History
DepositionJan 30, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 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 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KARYOPHERIN ALPHA
B: NUCLEOPLASMIN


Theoretical massNumber of molelcules
Total (without water)48,9582
Polymers48,9582
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint0 kcal/mol
Surface area18470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.560, 63.700, 62.150
Angle α, β, γ (deg.)90.00, 97.34, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein KARYOPHERIN ALPHA


Mass: 46927.578 Da / Num. of mol.: 1 / Fragment: ARMADILLLO-REPEAT DOMAIN / Mutation: Y397D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q02821
#2: Protein/peptide NUCLEOPLASMIN


Mass: 2030.545 Da / Num. of mol.: 1 / Fragment: NLS (NUCLEAR LOCALIZATION SEQUENCE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / References: UniProt: P05221
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 %(w/v)PEG80001reservoir
2250 mM1reservoirKH2PO4
350 mMn-octylglucoside1reservoir
420 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 21907 / % possible obs: 90.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 32.7
Reflection shellResolution: 2.4→30 Å / Rmerge(I) obs: 0.286 / % possible all: 80
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 21907 / Num. measured all: 105706
Reflection shell
*PLUS
% possible obs: 80 % / Mean I/σ(I) obs: 4.6

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.4→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber /
RfactorSelection details
Rfree0.265 random 5%
Rwork0.241 -
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3310 0 0 32 3342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg3.45
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS

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