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- PDB-8gxr: crystal structure of UBC domain of UBE2O -

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Basic information

Entry
Database: PDB / ID: 8gxr
Titlecrystal structure of UBC domain of UBE2O
Components(E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
KeywordsCONTRACTILE PROTEIN / UBE2O / UBC domain
Function / homologyUBE2O, 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 / CITRIC ACID / (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
Function and homology information
Biological speciesTrametes pubescens (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFu, Z. / Zhu, W. / Huang, H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2025
Title: Structural insights into the biochemical mechanism of the E2/E3 hybrid enzyme UBE2O.
Authors: Huang, H. / Zhu, W. / Huang, B. / Fu, Z. / Xiong, Y. / Cao, D. / Ye, Y. / Chang, Q. / Li, W. / Li, L. / Zhou, H. / Niu, X. / Zhang, W.
History
DepositionSep 21, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
B: (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
C: (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
D: (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,5118
Polymers125,7424
Non-polymers7684
Water5,098283
1
A: (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6282
Polymers31,4361
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6282
Polymers31,4361
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6282
Polymers31,4361
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: (E3-independent) E2 ubiquitin-conjugating enzyme UBE2O
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6282
Polymers31,4361
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.390, 96.960, 207.130
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
(E3-independent) E2 ubiquitin-conjugating enzyme UBE2O


Mass: 31435.525 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trametes pubescens (fungus) / Gene: TRAPUB_10883 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1M2VY70
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.57 Å3/Da / Density % sol: 52.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.979191 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 1.7→38.09 Å / Num. obs: 143060 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 30.09 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.6
Reflection shellResolution: 1.7→1.74 Å / Num. unique obs: 10459 / CC1/2: 0.545

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Processing

Software
NameVersionClassification
xia2data scaling
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
PHENIXphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: none

Resolution: 1.7→38.09 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 7165 5.01 %
Rwork0.2246 135736 -
obs0.2258 142901 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 93.93 Å2 / Biso mean: 43.8553 Å2 / Biso min: 25.92 Å2
Refinement stepCycle: final / Resolution: 1.7→38.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8637 0 52 283 8972
Biso mean--45.59 42.99 -
Num. residues----1117
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.720.52382320.481944554687100
1.72-1.740.50692480.45945114759100
1.74-1.760.44732260.426944724698100
1.76-1.780.47592310.424644544685100
1.78-1.810.46542300.393945054735100
1.81-1.830.3912530.371144694722100
1.83-1.860.38182300.343744574687100
1.86-1.890.3722300.342145084738100
1.89-1.910.40522370.34744734710100
1.91-1.950.37342480.333145004748100
1.95-1.980.32312370.284544764713100
1.98-2.020.32472260.282745324758100
2.02-2.050.29812510.277244384689100
2.05-2.10.30312460.264545144760100
2.1-2.140.29322530.253644784731100
2.14-2.190.30042340.237844914725100
2.19-2.250.24662090.237345554764100
2.25-2.310.31832340.242745094743100
2.31-2.380.2722220.228445424764100
2.38-2.450.25922550.229444564711100
2.45-2.540.28352340.23445254759100
2.54-2.640.24432340.228645374771100
2.64-2.760.26112590.222245154774100
2.76-2.910.25312470.240345364783100
2.91-3.090.29022300.240145794809100
3.09-3.330.27142280.230545634791100
3.33-3.660.23712420.211845824824100
3.66-4.190.19962580.175546044862100
4.19-5.280.1812390.172746894928100
5.28-38.090.18432620.17854811507399

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