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- PDB-9quf: Structure of a fungal Ube2O -

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Basic information

Entry
Database: PDB / ID: 9quf
TitleStructure of a fungal Ube2O
ComponentsUbiquitin-conjugating enzyme
KeywordsLIGASE / E2/E3 enzyme
Function / homologyUBE2O, tandem tSH3-B domain / UBE2O, SH3-B domain / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / ubiquitin conjugating enzyme activity / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme/RWD-like / Ubiquitin-conjugating enzyme
Function and homology information
Biological speciesPyrenophora tritici-repentis (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsKordic, D. / Williams, T.L. / Luiza Deszcz, L. / Ehrmann, J. / Arnese, R. / Meinhart, A. / Clausen, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Biol.Chem. / Year: 2025
Title: Structural basis for substrate recruitment and catalytic ubiquitin transfer by the E2/E3 hybrid enzyme UBE2O.
Authors: Kordic, D. / Williams, T.L. / Deszcz, L. / Ehrmann, J.F. / Arnese, R. / Schleiffer, A. / Clausen, T. / Meinhart, A.
History
DepositionApr 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-conjugating enzyme


Theoretical massNumber of molelcules
Total (without water)97,7211
Polymers97,7211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: s
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)154.010, 154.010, 90.670
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Ubiquitin-conjugating enzyme


Mass: 97721.211 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrenophora tritici-repentis (fungus) / Gene: Ptr86124_001839 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A922SUA0
Has protein modificationY

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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: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 5% (w/v) PEG8000, 1M Li2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.9786 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3→99 Å / Num. obs: 48136 / % possible obs: 99.5 % / Redundancy: 10.3 % / CC1/2: 1 / Net I/σ(I): 29.4
Reflection shellResolution: 3→3.07 Å / Mean I/σ(I) obs: 4.91 / Num. unique obs: 3369 / CC1/2: 0.937

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL2Mapphasing
XSCALEdata scaling
XDSdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3→44.46 Å / SU ML: 0.518 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.5215
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2874 1235 5 %
Rwork0.2286 23447 -
obs0.2315 24682 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 83.12 Å2
Refinement stepCycle: LAST / Resolution: 3→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6090 0 0 0 6090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036225
X-RAY DIFFRACTIONf_angle_d0.54498468
X-RAY DIFFRACTIONf_chiral_restr0.0449959
X-RAY DIFFRACTIONf_plane_restr0.0041097
X-RAY DIFFRACTIONf_dihedral_angle_d15.64532295
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.120.45251320.40772496X-RAY DIFFRACTION96.23
3.12-3.260.37511370.28782614X-RAY DIFFRACTION100
3.26-3.430.3021370.25932600X-RAY DIFFRACTION100
3.43-3.640.31131360.25262592X-RAY DIFFRACTION100
3.64-3.920.33071380.25572612X-RAY DIFFRACTION100
3.92-4.320.31081370.2052609X-RAY DIFFRACTION100
4.32-4.940.24361380.1922628X-RAY DIFFRACTION100
4.94-6.220.25591380.22552613X-RAY DIFFRACTION100
6.23-44.460.26071420.20632683X-RAY DIFFRACTION99.79

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