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- PDB-5h2v: Crystal structure of the karyopherin Kap121p bound to the SUMO pr... -

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Basic information

Entry
Database: PDB / ID: 5h2v
TitleCrystal structure of the karyopherin Kap121p bound to the SUMO protease Ulp1p
Components
  • Importin subunit beta-3
  • Ubiquitin-like-specific protease 1
KeywordsPROTEIN TRANSPORT/HYDROLASE / nuclear import / PROTEIN TRANSPORT-HYDROLASE complex
Function / homology
Function and homology information


Ulp1 peptidase / regulation of protein desumoylation / SUMO is proteolytically processed / deSUMOylase activity / protein desumoylation / nuclear import signal receptor activity / regulation of mitotic nuclear division / nuclear localization sequence binding / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA export from nucleus ...Ulp1 peptidase / regulation of protein desumoylation / SUMO is proteolytically processed / deSUMOylase activity / protein desumoylation / nuclear import signal receptor activity / regulation of mitotic nuclear division / nuclear localization sequence binding / Major pathway of rRNA processing in the nucleolus and cytosol / mRNA export from nucleus / cysteine-type peptidase activity / protein import into nucleus / G2/M transition of mitotic cell cycle / nuclear envelope / protein-containing complex binding / nucleolus / proteolysis / nucleus / cytoplasm
Similarity search - Function
Importin repeat / Importin repeat 6 / Importin repeat 4 / Importin repeat / Importin repeat / Importin repeat 6 / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Importin beta family ...Importin repeat / Importin repeat 6 / Importin repeat 4 / Importin repeat / Importin repeat / Importin repeat 6 / Ubiquitin-like protease family profile. / Ulp1 protease family, C-terminal catalytic domain / Ulp1 protease family, C-terminal catalytic domain / Importin beta family / HEAT-like repeat / 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
Importin subunit beta-3 / Ubiquitin-like-specific protease 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsKobayashi, J. / 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 2.0Feb 26, 2020Group: Data collection / Polymer sequence / Category: diffrn_source / entity_poly
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_target_identifier
Revision 2.1Nov 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: Ubiquitin-like-specific protease 1


Theoretical massNumber of molelcules
Total (without water)137,1492
Polymers137,1492
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-1 kcal/mol
Surface area44930 Å2
Unit cell
Length a, b, c (Å)76.830, 124.710, 130.000
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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: PSE1, KAP121, YMR308C, YM9952.10C / Production host: Escherichia coli (E. coli) / References: UniProt: P32337
#2: Protein Ubiquitin-like-specific protease 1


Mass: 17237.002 Da / Num. of mol.: 1 / Fragment: UNP residues 1-150
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

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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: 2.27 Å3/Da / Density % sol: 45.83 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M HEPES, 10% 2-propanol, 24% PEG20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→36.71 Å / Num. obs: 31520 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 45.26 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.167 / Rpim(I) all: 0.067 / Rrim(I) all: 0.18 / Net I/σ(I): 8.4 / Num. measured all: 224445 / Scaling rejects: 5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.8-2.957.20.7280.7781100
8.85-36.716.40.050.997198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimless0.1.27data scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
MOLREPphasing
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W3W

3w3w


Resolution: 2.8→36.713 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2412 1594 5.07 %
Rwork0.1979 --
obs0.2001 31460 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→36.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7988 0 0 0 7988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058123
X-RAY DIFFRACTIONf_angle_d0.88911040
X-RAY DIFFRACTIONf_dihedral_angle_d14.4132938
X-RAY DIFFRACTIONf_chiral_restr0.0321332
X-RAY DIFFRACTIONf_plane_restr0.0041398
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.89030.30821520.27022665X-RAY DIFFRACTION100
2.8903-2.99360.32471320.26312686X-RAY DIFFRACTION100
2.9936-3.11340.28371270.23762694X-RAY DIFFRACTION100
3.1134-3.2550.29141250.22932687X-RAY DIFFRACTION100
3.255-3.42650.25631210.212714X-RAY DIFFRACTION100
3.4265-3.6410.23041760.19832665X-RAY DIFFRACTION100
3.641-3.92180.24131680.18562660X-RAY DIFFRACTION100
3.9218-4.3160.23141600.16982704X-RAY DIFFRACTION100
4.316-4.93920.19991630.16672708X-RAY DIFFRACTION100
4.9392-6.2180.23431470.20372766X-RAY DIFFRACTION100
6.218-36.71590.21211230.182917X-RAY DIFFRACTION100
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)
11.83311.19310.72241.95840.00271.8918-0.19390.394-0.0007-0.35330.16850.2654-0.10510.27990.03730.5067-0.0769-0.07640.5163-0.05170.28758.60254.6798-63.1704
21.8835-0.50020.44970.9065-0.14093.05890.08360.3271-0.3227-0.15510.07010.0780.09210.4544-0.07810.30980.0486-0.0090.4204-0.10230.199123.96156.9992-45.51
33.317-0.7803-1.01291.26610.61281.06720.005-0.26750.2959-0.0930.00460.0476-0.04140.1745-0.02120.2523-0.0175-0.00610.2634-0.04160.201113.780518.8437-19.5298
41.80950.04-1.76481.674-0.13211.47310.1097-0.66960.2923-0.0285-0.11190.0188-0.1380.3330.0360.2391-0.1004-0.01820.4927-0.14750.2708-0.071422.8925-5.2123
52.74360.9588-0.26590.75170.35641.30420.023-0.10140.3267-0.01180.03570.1770.031-0.0439-0.02310.19730.02020.0320.1416-0.09580.2707-26.395617.7059-9.1919
62.60050.3359-0.69641.5770.43250.99610.41850.35110.3805-0.555-0.1936-0.5714-0.3830.22080.08260.5172-0.07670.42050.46090.16490.6161-16.93933.9173-35.2611
71.4046-1.71480.2391.8720.06851.53140.20370.3361-0.1171-0.2098-0.1028-0.33410.27940.1655-0.0560.39150.04450.07520.2896-0.11780.5168-18.5222-13.3207-26.5853
80.2410.59650.23290.57620.1007-0.052-0.09310.0276-0.65290.001-0.16710.11450.05420.31140.02130.5580.00750.08340.75190.07550.8129.5938-10.8947-19.819
91.7359-0.1980.45160.55830.02921.12140.0113-0.2691-0.1768-0.1919-0.1003-0.45350.36370.1858-0.01890.67090.2007-0.06620.5965-0.03470.9811-2.82-25.4297-14.0876
101.51090.1176-0.17311.03090.32482.05240.0367-0.151-0.32120.2132-0.1837-0.15860.25170.07270.12140.84280.0442-0.24460.56160.00170.9627-9.4774-25.292210.1283
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:74)
2X-RAY DIFFRACTION2(chain A and resid 75:203)
3X-RAY DIFFRACTION3(chain A and resid 204:337)
4X-RAY DIFFRACTION4(chain A and resid 338:419)
5X-RAY DIFFRACTION5(chain A and resid 420:614)
6X-RAY DIFFRACTION6(chain A and resid 615:664)
7X-RAY DIFFRACTION7(chain A and resid 665:799)
8X-RAY DIFFRACTION8(chain A and resid 800:830)
9X-RAY DIFFRACTION9(chain A and resid 831:891)
10X-RAY DIFFRACTION10(chain A and resid 892:1088)

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