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- PDB-1bk5: KARYOPHERIN ALPHA FROM SACCHAROMYCES CEREVISIAE -

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Basic information

Entry
Database: PDB / ID: 1bk5
TitleKARYOPHERIN ALPHA FROM SACCHAROMYCES CEREVISIAE
ComponentsKARYOPHERIN ALPHA
KeywordsPROTEIN TRANSPORT / NLS NUCLEAR IMPORT / ARMADILLO REPEAT CONTAINING PROTEIN
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 / MIR (MIR) / Resolution: 2.2 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 6, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KARYOPHERIN ALPHA
B: KARYOPHERIN ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5554
Polymers93,4372
Non-polymers1182
Water4,143230
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.980, 74.140, 84.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99774, 0.06554, -0.01504), (0.06667, 0.99328, -0.09458), (0.00874, -0.09537, -0.9954)
Vector: 156.60905, -0.28178, 103.04947)

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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 / 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: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / 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 %PEG40001reservoir
2200 mMsodium acetate1reservoir
3100 mMHEPES1reservoir
420 mM1reservoirCoCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9
DetectorType: BRANDEIS / Detector: CCD / Date: Feb 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→19.5 Å / Num. obs: 48255 / % possible obs: 95 % / Rsym value: 0.065 / Net I/σ(I): 13.6
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.8 / Rsym value: 0.299 / % possible all: 95
Reflection
*PLUS
Num. measured all: 525332 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 95 % / Rmerge(I) obs: 0.299

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR (MIR) / Resolution: 2.2→19.5 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.276 -4 %RANDOM
Rwork0.237 ---
obs0.237 48255 95 %-
Solvent computationSolvent model: FLAT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-13.224 Å20 Å20 Å2
2---26.797 Å20 Å2
3---13.574 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6550 0 2 230 6782
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.37
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.827
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: 2.2→2.22 Å / Total num. of bins used: 38
RfactorNum. reflection% reflection
Rfree0.327 -3.7 %
Rwork0.356 1168 -
obs--95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: CNS / Version: 0.3 / 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_deg17.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.827
LS refinement shell
*PLUS
Rfactor obs: 0.356

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