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- PDB-3w3x: Crystal structure of Kap121p bound to Pho4p -

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Basic information

Entry
Database: PDB / ID: 3w3x
TitleCrystal structure of Kap121p bound to Pho4p
Components
  • Importin subunit beta-3
  • Phosphate system positive regulatory protein PHO4
KeywordsPROTEIN TRANSPORT/TRANSCRIPTION / HEAT repeat / nuclear import / PROTEIN TRANSPORT-TRANSCRIPTION complex
Function / homology
Function and homology information


positive regulation of phosphate metabolic process / regulation of protein desumoylation / nuclear localization sequence binding / cellular response to phosphate starvation / nuclear import signal receptor activity / regulation of mitotic nuclear division / mRNA export from nucleus / protein import into nucleus / sequence-specific DNA binding / protein dimerization activity ...positive regulation of phosphate metabolic process / regulation of protein desumoylation / nuclear localization sequence binding / cellular response to phosphate starvation / nuclear import signal receptor activity / regulation of mitotic nuclear division / mRNA export from nucleus / protein import into nucleus / sequence-specific DNA binding / protein dimerization activity / chromatin remodeling / DNA-binding transcription factor activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytoplasm
Similarity search - Function
Helix Hairpins - #1700 / Importin repeat / Importin repeat 6 / Importin repeat 4 / Importin repeat / Importin repeat / Importin repeat 6 / Importin beta family / HEAT-like repeat / Helix-loop-helix DNA-binding domain ...Helix Hairpins - #1700 / Importin repeat / Importin repeat 6 / Importin repeat 4 / Importin repeat / Importin repeat / Importin repeat 6 / Importin beta family / HEAT-like repeat / Helix-loop-helix DNA-binding domain / Helix Hairpins / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / Helix non-globular / Special / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Phosphate system positive regulatory protein PHO4 / Importin subunit beta-3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 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: Phosphate system positive regulatory protein PHO4


Theoretical massNumber of molelcules
Total (without water)122,8512
Polymers122,8512
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)78.090, 126.310, 128.050
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 Phosphate system positive regulatory protein PHO4


Mass: 2938.281 Da / Num. of mol.: 1 / Fragment: UNP residues 140-166 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P07270

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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: 2.57 Å3/Da / Density % sol: 52.14 %
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: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jul 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→29.97 Å / Num. all: 28698 / Num. obs: 28382 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→3.08 Å / % possible all: 96.9

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Processing

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

3w3t


Resolution: 2.9→29.5 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.886 / SU B: 18.531 / SU ML: 0.35 / Cross valid method: THROUGHOUT / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26823 1426 5 %RANDOM
Rwork0.22435 ---
all0.22654 28698 --
obs0.22654 26917 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.84 Å2
Baniso -1Baniso -2Baniso -3
1--3.93 Å20 Å20 Å2
2--4.76 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7849 0 0 0 7849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197982
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.97210876
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51751016
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.10325.5320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.716151310
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0721524
X-RAY DIFFRACTIONr_chiral_restr0.1030.21332
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215869
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: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 92 -
Rwork0.34 1907 -
obs--96.15 %

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