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- PDB-4zj7: Crystal structure of the karyopherin Kap121p bound to the extreme... -

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Basic information

Entry
Database: PDB / ID: 4zj7
TitleCrystal structure of the karyopherin Kap121p bound to the extreme C-terminus of the protein phosphatase Cdc14p
Components
  • Importin subunit beta-3
  • Tyrosine-protein phosphatase CDC14
KeywordsPROTEIN TRANSPORT/HYDROLASE / karyopherin / PROTEIN TRANSPORT-HYDROLASE complex
Function / homology
Function and homology information


RENT complex / new mitotic spindle pole body / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of mitotic actomyosin contractile ring assembly / meiotic spindle disassembly / meiotic nuclear division / regulation of protein desumoylation / mitotic spindle pole body / rDNA chromatin condensation / positive regulation of autophagosome assembly ...RENT complex / new mitotic spindle pole body / Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase / positive regulation of mitotic actomyosin contractile ring assembly / meiotic spindle disassembly / meiotic nuclear division / regulation of protein desumoylation / mitotic spindle pole body / rDNA chromatin condensation / positive regulation of autophagosome assembly / regulation of exit from mitosis / cellular bud neck / autophagy of mitochondrion / rDNA heterochromatin formation / nuclear localization sequence binding / spindle pole body / cellular response to osmotic stress / nuclear import signal receptor activity / negative regulation of transcription by RNA polymerase I / regulation of mitotic nuclear division / positive regulation of cytokinesis / MAPK6/MAPK4 signaling / protein serine/threonine phosphatase activity / phosphoprotein phosphatase activity / mRNA export from nucleus / protein-tyrosine-phosphatase / positive regulation of autophagy / protein tyrosine phosphatase activity / chromosome segregation / microtubule cytoskeleton organization / protein import into nucleus / spindle pole / mitotic spindle / mitotic cell cycle / cell division / nucleolus / nucleus / cytoplasm
Similarity search - Function
Helix Hairpins - #1700 / Dual specificity/tyrosine protein phosphatase, N-terminal / Dual-specificity phosphatase CDC14, C-terminal / Dual specificity protein phosphatase, N-terminal half / Importin repeat / Importin repeat 6 / Importin repeat 4 / Importin repeat / Importin repeat / Importin repeat 6 ...Helix Hairpins - #1700 / Dual specificity/tyrosine protein phosphatase, N-terminal / Dual-specificity phosphatase CDC14, C-terminal / Dual specificity protein phosphatase, N-terminal half / Importin repeat / Importin repeat 6 / Importin repeat 4 / Importin repeat / Importin repeat / Importin repeat 6 / : / Importin beta family / HEAT-like repeat / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity phosphatase, catalytic domain / Dual specificity protein phosphatase domain profile. / Dual specificity protein phosphatase domain / Helix Hairpins / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine specific protein phosphatases domain profile. / Tyrosine-specific protein phosphatases domain / Protein-tyrosine phosphatase-like / Helix non-globular / Special / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Importin subunit beta-3 / Tyrosine-protein phosphatase CDC14
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKobayashi, J. / Hirano, H. / Matsuura, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25440019 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2015
Title: Crystal structure of the karyopherin Kap121p bound to the extreme C-terminus of the protein phosphatase Cdc14p
Authors: Kobayashi, J. / Hirano, H. / Matsuura, Y.
History
DepositionApr 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jul 1, 2015Group: Database references
Revision 1.3Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Nov 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Importin subunit beta-3
B: Tyrosine-protein phosphatase CDC14


Theoretical massNumber of molelcules
Total (without water)123,7442
Polymers123,7442
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-2 kcal/mol
Surface area44790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.263, 127.758, 131.789
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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 / Mutation: residues 80-90 deleted
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PSE1, KAP121, YMR308C, YM9952.10C / Plasmid: pGEX-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: P32337
#2: Protein/peptide Tyrosine-protein phosphatase CDC14


Mass: 3831.567 Da / Num. of mol.: 1 / Fragment: UNP residues 517-551
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: CDC14, OAF3, YFR028C / Plasmid: pET30a-TEV / Production host: Escherichia coli (E. coli) / References: UniProt: Q00684, protein-tyrosine-phosphatase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.63 Å3/Da / Density % sol: 53.2 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 20000, 2-propanol

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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: Dec 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→26.36 Å / Num. obs: 51446 / % possible obs: 99.5 % / Redundancy: 4.3 % / Biso Wilson estimate: 46.72 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.058 / Net I/σ(I): 7.2 / Num. measured all: 220860 / Scaling rejects: 65
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.4-2.474.20.5991.61836043990.7530.33399.7
9.9-26.363.40.03818.822236600.9710.02380.9

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Processing

Software
NameVersionClassification
MOSFLMdata collection
Aimless0.3.11data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
Cootmodel building
MOLREPphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W3X

3w3x


Resolution: 2.4→25.814 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.93 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2519 2595 5.05 %
Rwork0.2189 48783 -
obs0.2206 51378 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.85 Å2 / Biso mean: 66.3712 Å2 / Biso min: 21.01 Å2
Refinement stepCycle: final / Resolution: 2.4→25.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7808 0 0 139 7947
Biso mean---50.89 -
Num. residues----1022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037941
X-RAY DIFFRACTIONf_angle_d0.77410817
X-RAY DIFFRACTIONf_chiral_restr0.0271322
X-RAY DIFFRACTIONf_plane_restr0.0041370
X-RAY DIFFRACTIONf_dihedral_angle_d14.3012819
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.44360.35851450.28792506265199
2.4436-2.49060.30531390.26625562695100
2.4906-2.54140.28841190.250525272646100
2.5414-2.59660.26761370.243825522689100
2.5966-2.65690.29251300.242525722702100
2.6569-2.72330.28531360.239325562692100
2.7233-2.79680.26291240.237825462670100
2.7968-2.8790.25851440.254425702714100
2.879-2.97180.30291450.253925642709100
2.9718-3.07790.31411130.243625902703100
3.0779-3.20090.26481240.244125592683100
3.2009-3.34630.26471300.24125792709100
3.3463-3.52230.28291170.242925982715100
3.5223-3.74240.24751750.222225422717100
3.7424-4.03030.26021640.202825612725100
4.0303-4.43410.19641510.185225722723100
4.4341-5.07150.21211490.17962599274899
5.0715-6.37360.26131420.2212632277499
6.3736-25.81560.21371110.19212602271393
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.0331-1.5659-1.19356.1295-0.41222.14990.27570.672-0.0208-0.8470.4395-0.0723-0.1520.0925-0.6520.805-0.46350.05151.9285-0.22680.53316.08041.6313-72.8925
24.30831.84532.99532.44921.42253.9405-0.07420.4674-0.2883-0.2690.33250.0137-0.01630.5795-0.21270.50740.0116-0.00420.6778-0.08460.349215.7744.4843-57.1868
33.75850.1992-0.5772.28071.09333.42980.05910.14820.089-0.2385-0.06610.057-0.1710.15290.00060.3252-0.018-0.00770.3572-0.01370.246722.344814.1328-29.1371
43.796-0.0055-2.25591.62320.01121.67270.0861-0.73660.45310.08220.0484-0.0185-0.24050.4293-0.12130.3061-0.0774-0.0220.4537-0.16490.3221-0.618722.9102-7.6666
54.49871.89020.61840.87180.30212.1362-0.0965-0.0630.4585-0.09450.04940.0976-0.1921-0.06570.03570.28010.05460.0080.2031-0.05550.3436-30.236216.8498-10.824
62.29080.9466-0.28371.8395-0.43431.82730.05090.41770.3461-0.4935-0.0799-1.0266-0.02260.93380.05110.57360.01840.27570.8430.0430.8758-13.06623.9501-37.1329
73.2771-2.3525-0.04523.3307-0.26452.45740.17030.4128-0.3918-0.1743-0.0477-0.50890.68620.4978-0.08430.58510.1233-0.02840.4656-0.1890.6616-17.0381-13.944-25.637
80.3848-1.0871.04838.8333.35129.3787-0.529-0.198-1.21480.1983-0.58260.33610.4556-0.19440.97780.5189-0.050.05620.72590.05080.651618.5615-1.9299-16.8298
92.2696-0.31930.61760.662-0.31673.00650.0645-0.6582-0.72270.05420.1304-0.91880.6110.8189-0.13560.8330.3463-0.23970.9374-0.10841.1764-0.8874-24.3995-10.3289
101.8332-0.7144-0.63381.57460.41772.898-0.0344-0.1436-0.2673-0.0537-0.18040.15460.83810.2630.17921.00730.1223-0.24660.7865-0.01170.8585-13.3544-24.742514.1061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 3:8)A3 - 8
2X-RAY DIFFRACTION2(chain A and resid 9:150)A9 - 150
3X-RAY DIFFRACTION3(chain A and resid 151:278)A151 - 278
4X-RAY DIFFRACTION4(chain A and resid 279:449)A279 - 449
5X-RAY DIFFRACTION5(chain A and resid 450:619)A450 - 619
6X-RAY DIFFRACTION6(chain A and resid 620:664)A620 - 664
7X-RAY DIFFRACTION7(chain A and resid 665:810)A665 - 810
8X-RAY DIFFRACTION8(chain A and resid 811:822)A811 - 822
9X-RAY DIFFRACTION9(chain A and resid 826:919)A826 - 919
10X-RAY DIFFRACTION10(chain A and resid 920:1089)A920 - 1089

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