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- PDB-5h2x: Crystal structure of the karyopherin Kap60p bound to the SUMO pro... -

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Basic information

Entry
Database: PDB / ID: 5h2x
TitleCrystal structure of the karyopherin Kap60p bound to the SUMO protease Ulp1p (150-172)
Components
  • Importin subunit alpha
  • Ubiquitin-like-specific protease 1
KeywordsPROTEIN TRANSPORT/HYDROGENASE / nuclear import / PROTEIN TRANSPORT-HYDROGENASE 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 / Resolution: 2.2 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


Theoretical massNumber of molelcules
Total (without water)49,6572
Polymers49,6572
Non-polymers00
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint0 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.570, 77.480, 114.590
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 alpha / Karyopherin subunit alpha / Karyopherin-60 / Serine-rich RNA polymerase I suppressor protein


Mass: 46847.535 Da / Num. of mol.: 1 / 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/peptide Ubiquitin-like-specific protease 1


Mass: 2809.191 Da / Num. of mol.: 1 / Fragment: UNP residues 150-172
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.: 220 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M sodium phosphate, 12% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.2→49.27 Å / Num. obs: 25386 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 25.26 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.065 / Rrim(I) all: 0.16 / Net I/σ(I): 9.9 / Num. measured all: 149220 / Scaling rejects: 69
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.2-2.276.10.7870.7771100
9.07-49.274.80.0380.998199.6

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Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H2W

5h2w


Resolution: 2.2→49.268 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.15
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2284 1276 5.04 %
Rwork0.2016 --
obs0.203 25326 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.79 Å2 / Biso mean: 32.3559 Å2 / Biso min: 13.42 Å2
Refinement stepCycle: final / Resolution: 2.2→49.268 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3412 0 0 220 3632
Biso mean---34.19 -
Num. residues----437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033467
X-RAY DIFFRACTIONf_angle_d0.7384711
X-RAY DIFFRACTIONf_chiral_restr0.025556
X-RAY DIFFRACTIONf_plane_restr0.004607
X-RAY DIFFRACTIONf_dihedral_angle_d14.2251304
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2001-2.28820.30231310.245426212752
2.2882-2.39230.26141370.226326262763
2.3923-2.51840.24711410.226226322773
2.5184-2.67620.26111450.222326292774
2.6762-2.88280.28031480.219826602808
2.8828-3.17290.26241430.218526442787
3.1729-3.63190.23851390.205726982837
3.6319-4.57530.18441420.167327012843
4.5753-49.28080.17821500.182328392989

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