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- PDB-5h2w: Crystal structure of the karyopherin Kap60p bound to the SUMO pro... -

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Basic information

Entry
Database: PDB / ID: 5h2w
TitleCrystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-340)
Components
  • Importin subunit alpha
  • Ubiquitin-like-specific protease 1
KeywordsPROTEIN TRANSPORT/HYDROLASE / nuclear import / PROTEIN TRANSPORT-HYDROLASE complex
Function / homology
Function and homology information


Ulp1 peptidase / proteasome localization / deSUMOylase activity / protein desumoylation / SUMO is proteolytically processed / import into nucleus / NLS-dependent protein nuclear import complex / NLS-bearing protein import into nucleus / nuclear localization sequence binding / nuclear import signal receptor activity ...Ulp1 peptidase / proteasome localization / deSUMOylase activity / protein desumoylation / SUMO is proteolytically processed / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / cysteine-type peptidase activity / G2/M transition of mitotic cell cycle / protein import into nucleus / disordered domain specific binding / nuclear envelope / protein-containing complex binding / nucleolus / perinuclear region of cytoplasm / protein-containing complex / proteolysis / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / 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. ...Ulp1 protease family, C-terminal catalytic domain / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / 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 / Papain-like cysteine peptidase superfamily / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Ubiquitin-like-specific protease 1 / Importin subunit alpha
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsHirano, H. / Matsuura, Y.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS25440019 Japan
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structures of the Karyopherins Kap121p and Kap60p Bound to the Nuclear Pore-Targeting Domain of the SUMO Protease Ulp1p
Authors: Hirano, H. / Kobayashi, J. / Matsuura, Y.
History
DepositionOct 18, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2017Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
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
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 alpha
B: Ubiquitin-like-specific protease 1
C: Importin subunit alpha
D: Ubiquitin-like-specific protease 1


Theoretical massNumber of molelcules
Total (without water)137,9414
Polymers137,9414
Non-polymers00
Water1,53185
1
A: Importin subunit alpha
B: Ubiquitin-like-specific protease 1


Theoretical massNumber of molelcules
Total (without water)68,9702
Polymers68,9702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-1 kcal/mol
Surface area18630 Å2
MethodPISA
2
C: Importin subunit alpha
D: Ubiquitin-like-specific protease 1


Theoretical massNumber of molelcules
Total (without water)68,9702
Polymers68,9702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-0 kcal/mol
Surface area18440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.610, 63.540, 80.910
Angle α, β, γ (deg.)106.09, 107.72, 90.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Importin subunit alpha / Karyopherin subunit alpha / Karyopherin-60 / Serine-rich RNA polymerase I suppressor protein


Mass: 46847.535 Da / Num. of mol.: 2 / Fragment: UNP residues 88-510
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: SRP1, KAP60, YNL189W, N1606 / Production host: Escherichia coli (E. coli) / References: UniProt: Q02821
#2: Protein Ubiquitin-like-specific protease 1


Mass: 22122.736 Da / Num. of mol.: 2 / Fragment: UNP residues 150-340
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ULP1, YPL020C, LPB11C / Production host: Escherichia coli (E. coli) / References: UniProt: Q02724, Ulp1 peptidase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 1.79 Å3/Da / Density % sol: 31.1 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1M MES, 0.1M calcium acetate, 12% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→30.37 Å / Num. obs: 29881 / % possible obs: 90.5 % / Redundancy: 1.6 % / Biso Wilson estimate: 29.84 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.05 / Rrim(I) all: 0.07 / Net I/σ(I): 5.9 / Num. measured all: 47966
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.5-2.61.70.1630.956191
9.01-30.371.90.0250.996191.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.5.8data scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C1T

2c1t


Resolution: 2.5→27.028 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2466 1542 5.16 %
Rwork0.2135 --
obs0.2152 29866 90.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→27.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6667 0 0 85 6752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036775
X-RAY DIFFRACTIONf_angle_d0.8229219
X-RAY DIFFRACTIONf_dihedral_angle_d14.0022507
X-RAY DIFFRACTIONf_chiral_restr0.0281104
X-RAY DIFFRACTIONf_plane_restr0.0041180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58060.32321510.28492600X-RAY DIFFRACTION91
2.5806-2.67280.32851530.27762519X-RAY DIFFRACTION89
2.6728-2.77970.29381570.26142570X-RAY DIFFRACTION90
2.7797-2.90610.29251010.26162597X-RAY DIFFRACTION90
2.9061-3.05910.29111290.24852508X-RAY DIFFRACTION88
3.0591-3.25050.25351370.23672584X-RAY DIFFRACTION91
3.2505-3.50090.25941530.23232585X-RAY DIFFRACTION91
3.5009-3.85240.2611550.20322524X-RAY DIFFRACTION90
3.8524-4.40770.19311300.17272540X-RAY DIFFRACTION89
4.4077-5.54540.20871520.192545X-RAY DIFFRACTION90
5.5454-27.02990.19751240.16732752X-RAY DIFFRACTION96

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