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- PDB-3w3y: Crystal structure of Kap121p bound to Nup53p -

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Basic information

Entry
Database: PDB / ID: 3w3y
TitleCrystal structure of Kap121p bound to Nup53p
Components
  • Importin subunit beta-3
  • Nucleoporin NUP53
KeywordsPROTEIN TRANSPORT/DNA BINDING PROTEIN / HEAT repeat / nuclear import / PROTEIN TRANSPORT-DNA BINDING PROTEIN complex
Function / homology
Function and homology information


response to spindle checkpoint signaling / regulation of protein desumoylation / nuclear pore central transport channel / nuclear pore organization / nuclear pore nuclear basket / protein localization to kinetochore / NLS-bearing protein import into nucleus / nuclear localization sequence binding / structural constituent of nuclear pore / nuclear import signal receptor activity ...response to spindle checkpoint signaling / regulation of protein desumoylation / nuclear pore central transport channel / nuclear pore organization / nuclear pore nuclear basket / protein localization to kinetochore / NLS-bearing protein import into nucleus / nuclear localization sequence binding / structural constituent of nuclear pore / nuclear import signal receptor activity / nucleocytoplasmic transport / regulation of mitotic nuclear division / mRNA transport / nuclear pore / mRNA export from nucleus / phospholipid binding / protein import into nucleus / nuclear envelope / single-stranded DNA binding / nuclear membrane / cell division / positive regulation of DNA-templated transcription / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Helix Hairpins - #1700 / Importin repeat / Importin repeat 6 / Importin repeat 4 / Importin repeat / Importin repeat / Importin repeat 6 / RNA-recognition motif (RRM) Nup35-type domain / Nup53/35/40-type RNA recognition motif / RNA-recognition motif (RRM) Nup35-type domain profile. ...Helix Hairpins - #1700 / Importin repeat / Importin repeat 6 / Importin repeat 4 / Importin repeat / Importin repeat / Importin repeat 6 / RNA-recognition motif (RRM) Nup35-type domain / Nup53/35/40-type RNA recognition motif / RNA-recognition motif (RRM) Nup35-type domain profile. / Importin beta family / HEAT-like repeat / Helix Hairpins / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Helix non-globular / Special / RNA-binding domain superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily / Mainly Alpha
Similarity search - Domain/homology
Importin subunit beta-3 / Nucleoporin NUP53
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKobayashi, J. / Matsuura, Y.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Structural basis for cell-cycle-dependent nuclear import mediated by the karyopherin Kap121p.
Authors: Kobayashi, J. / Matsuura, Y.
History
DepositionDec 28, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Importin subunit beta-3
B: Nucleoporin NUP53


Theoretical massNumber of molelcules
Total (without water)125,4142
Polymers125,4142
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1120 Å2
ΔGint1 kcal/mol
Surface area44740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.330, 131.440, 131.500
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 Importin subunit beta-3 / Karyopherin subunit beta-3 / Karyopherin-121 / Protein secretion enhancer 1


Mass: 119912.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: PSE1, KAP121, YMR308C, YM9952.10C / Production host: Escherichia coli (E. coli) / References: UniProt: P32337
#2: Protein/peptide Nucleoporin NUP53 / Nuclear pore protein NUP53


Mass: 5501.270 Da / Num. of mol.: 1 / Fragment: UNP residues 401-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NUP53, YMR153W, YM8520.02 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03790

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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: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M HEPES, 10% 2-propanol, 24% PEG 20000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 11, 2011
RadiationMonochromator: rotated-inclined double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30.99 Å / Num. all: 33972 / Num. obs: 32341 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.8→2.94 Å / % possible all: 79.2

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3W3T

3w3t


Resolution: 2.8→30.33 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.888 / SU B: 20.941 / SU ML: 0.392 / Cross valid method: THROUGHOUT / ESU R Free: 0.436 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.29672 1633 5.1 %RANDOM
Rwork0.25082 ---
all0.25309 33972 --
obs0.25309 30646 94.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.549 Å2
Baniso -1Baniso -2Baniso -3
1--7.68 Å20 Å20 Å2
2---0.29 Å20 Å2
3---7.97 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7862 0 0 0 7862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197997
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.97210901
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.61351019
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.69925.392319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.899151302
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1381525
X-RAY DIFFRACTIONr_chiral_restr0.1060.21337
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215885
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 86 -
Rwork0.389 1723 -
obs--74.63 %

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