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- PDB-1bk6: KARYOPHERIN ALPHA (YEAST) + SV40 T ANTIGEN NLS -

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Basic information

Entry
Database: PDB / ID: 1bk6
TitleKARYOPHERIN ALPHA (YEAST) + SV40 T ANTIGEN NLS
Components
  • (LARGE T ANTIGEN) x 2
  • KARYOPHERIN ALPHA
KeywordsCOMPLEX (PROTEIN TRANSPORT/PEPTIDE) / PROTEIN TRANSPORT / NLS NUCLEAR IMPORT / ARMADILLO REPEAT CONTAINING PROTEIN / COMPLEX (PROTEIN TRANSPORT-PEPTIDE) / COMPLEX (PROTEIN TRANSPORT-PEPTIDE) complex
Function / homology
Function and homology information


proteasome localization / import into nucleus / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / nuclear import signal receptor activity / protein targeting to membrane / protein import into nucleus / disordered domain specific binding / nuclear envelope ...proteasome localization / import into nucleus / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / nuclear import signal receptor activity / protein targeting to membrane / protein import into nucleus / disordered domain specific binding / nuclear envelope / protein-containing complex binding / perinuclear region of cytoplasm / protein-containing complex / nucleoplasm / nucleus / cytoplasm / 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 / Armadillo/beta-catenin-like repeats ...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
Importin subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2.8 Å
AuthorsConti, E. / Uy, M. / Leighton, L. / Blobel, G. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystallographic analysis of the recognition of a nuclear localization signal by the nuclear import factor karyopherin alpha.
Authors: Conti, E. / Uy, M. / Leighton, L. / Blobel, G. / Kuriyan, J.
History
DepositionJul 14, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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 ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KARYOPHERIN ALPHA
C: LARGE T ANTIGEN
D: LARGE T ANTIGEN
B: KARYOPHERIN ALPHA
E: LARGE T ANTIGEN
F: LARGE T ANTIGEN


Theoretical massNumber of molelcules
Total (without water)95,9986
Polymers95,9986
Non-polymers00
Water21612
1
A: KARYOPHERIN ALPHA
C: LARGE T ANTIGEN
D: LARGE T ANTIGEN


Theoretical massNumber of molelcules
Total (without water)47,9993
Polymers47,9993
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KARYOPHERIN ALPHA
E: LARGE T ANTIGEN
F: LARGE T ANTIGEN


Theoretical massNumber of molelcules
Total (without water)47,9993
Polymers47,9993
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.120, 75.750, 84.460
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 KARYOPHERIN ALPHA / IMPORTIN ALPHA / SRP1P


Mass: 46718.426 Da / Num. of mol.: 2 / Fragment: ARMADILLO DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: W303 / Cell line: BL21 / Cellular location: CYTOPLASMIC/NUCLEAR / Gene: SRP1 / Plasmid: PPROEX-HTB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q02821
#2: Protein/peptide LARGE T ANTIGEN


Mass: 791.059 Da / Num. of mol.: 2 / Fragment: NLS (NUCLEAR LOCALIZATION SIGNAL)
Source method: isolated from a genetically manipulated source
Details: NLS PEPTIDE AT THE LARGER (FUNCTIONAL) BINDING SITE
#3: Protein/peptide LARGE T ANTIGEN


Mass: 489.608 Da / Num. of mol.: 2 / Fragment: NLS (NUCLEAR LOCALIZATION SIGNAL)
Source method: isolated from a genetically manipulated source
Details: NLS PEPTIDE AT THE SMALLER BINDING SITE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.6 Å3/Da / Density % sol: 50 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118-20 %(w/v)PEG40001reservoir
2200 mMsodium acetate1reservoir
3100 mMHEPES1reservoir
420 mM1reservoirCoCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9
DetectorType: BRANDEIS / Detector: CCD / Date: Dec 1, 1997
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.8→29.1 Å / Num. obs: 22717 / % possible obs: 86.9 % / Redundancy: 3.5 % / Rsym value: 0.064 / Net I/σ(I): 17.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 9.9 / Rsym value: 0.188 / % possible all: 82.2
Reflection
*PLUS
Num. measured all: 270860 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 82.2 % / Rmerge(I) obs: 0.188

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Processing

Software
NameVersionClassification
CNS0.2refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.2phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: UNLIGANDED KARYOPHERIN ALPHA

Resolution: 2.8→29.1 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.307 -3.5 %RANDOM
Rwork0.256 ---
obs0.256 22717 86.8 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.043 Å20 Å20 Å2
2---19.147 Å20 Å2
3---4.105 Å2
Refinement stepCycle: LAST / Resolution: 2.8→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6488 0 0 12 6500
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.45
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16.87
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.737
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.85 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.353 -3.5 %
Rwork0.296 1072 -
obs--82.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: CNS / Version: 0.2 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg16.87
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.737
LS refinement shell
*PLUS
Rfactor obs: 0.296

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