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- PDB-6q83: Crystal structure of the biportin Pdr6 in complex with UBC9 -

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Basic information

Entry
Database: PDB / ID: 6q83
TitleCrystal structure of the biportin Pdr6 in complex with UBC9
Components
  • Importin beta-like protein KAP122
  • UBC9
KeywordsPROTEIN TRANSPORT / Importin-Beta family / biportin / nuclear import / SUMOylation
Function / homology
Function and homology information


SUMO conjugating enzyme activity / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic spindle elongation / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / nuclear export signal receptor activity / SUMOylation of DNA replication proteins ...SUMO conjugating enzyme activity / SUMOylation of nuclear envelope proteins / SUMO is transferred from E1 to E2 (UBE2I, UBC9) / mitotic spindle elongation / SUMOylation of transcription factors / Postmitotic nuclear pore complex (NPC) reformation / SUMOylation of transcription cofactors / SUMOylation of DNA damage response and repair proteins / nuclear export signal receptor activity / SUMOylation of DNA replication proteins / SUMOylation of SUMOylation proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / SUMOylation of RNA binding proteins / Transferases; Acyltransferases; Aminoacyltransferases / nuclear export / SUMO transferase activity / SUMOylation of chromatin organization proteins / nuclear import signal receptor activity / regulation of cell size / protein sumoylation / condensed nuclear chromosome / protein import into nucleus / nuclear envelope / cell division / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Importin beta-like protein KAP122 / SUMO-conjugating enzyme UBC9
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.53 Å
AuthorsAksu, M. / Trakhanov, S. / Vera-Rodriguez, A. / Gorlich, D.
CitationJournal: J.Cell Biol. / Year: 2019
Title: Structural basis for the nuclear import and export functions of the biportin Pdr6/Kap122.
Authors: Aksu, M. / Trakhanov, S. / Vera Rodriguez, A. / Gorlich, D.
History
DepositionDec 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 12, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: 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 beta-like protein KAP122
B: UBC9


Theoretical massNumber of molelcules
Total (without water)141,3552
Polymers141,3552
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint4 kcal/mol
Surface area53710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.260, 198.260, 289.630
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Importin beta-like protein KAP122 / Karyopherin-122 / Pleiotropic drug resistance regulatory protein 6


Mass: 123492.633 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: KAP122, PDR6, YGL016W / Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 F' / References: UniProt: P32767
#2: Protein UBC9


Mass: 17862.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Plasmid: pQE-80 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB Express / References: UniProt: P50623

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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: 4.09 Å3/Da / Density % sol: 69.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7 / Details: Sodium cacodylate, magnesium chloride, ethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 4.53→49.565 Å / Num. obs: 12937 / % possible obs: 99.6 % / Redundancy: 10.072 % / Biso Wilson estimate: 226.685 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.168 / Rrim(I) all: 0.178 / Χ2: 0.989 / Net I/σ(I): 11.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.53-4.659.2252.4920.928920.5782.63895.7
4.65-4.7810.4382.0991.189290.6382.207100
4.78-4.9110.7441.7531.449050.6241.841100
4.91-5.0610.7341.6381.518720.6471.72100
5.06-5.2310.6431.4231.768490.7181.495100
5.23-5.4110.581.3231.898090.7071.3999.9
5.41-5.6210.4541.2631.987860.8161.328100
5.62-5.8510.3711.1132.237660.811.171100
5.85-6.1110.1940.9052.827370.8470.953100
6.11-6.419.7250.7823.267100.8680.82699.9
6.41-6.758.9280.5254.826690.9580.558100
6.75-7.169.5890.3297.746370.9820.348100
7.16-7.6610.5670.19612.845960.9910.207100
7.66-8.2710.3770.11620.595620.9970.122100
8.27-9.0610.0290.0730.115170.9990.074100
9.06-10.139.6480.04244.254690.9990.044100
10.13-11.79.2130.03948.624270.9990.041100
11.7-14.338.1890.03650.113540.9990.038100
14.33-20.269.990.03159.332860.9990.033100
20.26-49.5659.1090.02860.661650.9990.0394.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GJD and 6Q82

2gjd

6q82


Resolution: 4.53→49.565 Å / SU ML: 0.83 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 43.21
RfactorNum. reflection% reflection
Rfree0.2708 744 3.03 %
Rwork0.2593 --
obs0.2597 12912 99.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 351.26 Å2 / Biso mean: 311.3736 Å2 / Biso min: 289.44 Å2
Refinement stepCycle: final / Resolution: 4.53→49.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9380 0 0 0 9380
Num. residues----1168
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.5301-4.87960.38461450.38864668481398
4.8796-5.37010.33521520.378347874939100
5.3701-6.14590.4451470.390747514898100
6.1459-7.73840.34491470.339147924939100
7.7384-49.56790.20631530.189847914944100

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