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- PDB-9qug: Structure of a UBC-Ubiquitin conjugate -

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Basic information

Entry
Database: PDB / ID: 9qug
TitleStructure of a UBC-Ubiquitin conjugate
Components
  • (E3-independent) E2 ubiquitin-conjugating enzyme
  • Polyubiquitin-B
KeywordsLIGASE / E2/E3 enzyme UBC domain conjugated to ubiquitin
Function / homology
Function and homology information


(E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / hypothalamus gonadotrophin-releasing hormone neuron development / retrograde transport, endosome to Golgi / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development ...(E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / hypothalamus gonadotrophin-releasing hormone neuron development / retrograde transport, endosome to Golgi / female meiosis I / positive regulation of protein monoubiquitination / fat pad development / mitochondrion transport along microtubule / female gonad development / seminiferous tubule development / ubiquitin conjugating enzyme activity / male meiosis I / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein K63-linked ubiquitination / protein monoubiquitination / energy homeostasis / regulation of neuron apoptotic process / neuron projection morphogenesis / regulation of proteasomal protein catabolic process / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Pexophagy / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Regulation of BACH1 activity / Translesion synthesis by REV1 / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / positive regulation of protein ubiquitination / Translesion synthesis by POLK / InlB-mediated entry of Listeria monocytogenes into host cell / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Josephin domain DUBs / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / regulation of mitochondrial membrane potential / TNFR1-induced NF-kappa-B signaling pathway / Autodegradation of Cdh1 by Cdh1:APC/C / TCF dependent signaling in response to WNT / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / activated TAK1 mediates p38 MAPK activation / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of signaling by CBL / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Deactivation of the beta-catenin transactivating complex / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import
Similarity search - Function
UBE2O, ubiquitin binding SH3-C domain / UBE2O, N-terminal SH3-A domain / UBE2O, tandem tSH3-B domain / UBE2O, SH3-B domain / 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 / : ...UBE2O, ubiquitin binding SH3-C domain / UBE2O, N-terminal SH3-A domain / UBE2O, tandem tSH3-B domain / UBE2O, SH3-B domain / 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 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
polyethylene glycol / Polyubiquitin-B / (E3-independent) E2 ubiquitin-conjugating enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,6358
Polymers50,9412
Non-polymers1,6946
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-11 kcal/mol
Surface area16950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.577, 82.845, 98.657
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Polyubiquitin-B


Mass: 8576.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#2: Protein (E3-independent) E2 ubiquitin-conjugating enzyme / E2/E3 hybrid ubiquitin-protein ligase UBE2O / Ubiquitin carrier protein O / Ubiquitin-conjugating ...E2/E3 hybrid ubiquitin-protein ligase UBE2O / Ubiquitin carrier protein O / Ubiquitin-conjugating enzyme E2 O / Ubiquitin-conjugating enzyme E2 of 230 kDa / Ubiquitin-conjugating enzyme E2-230K / Ubiquitin-protein ligase O


Mass: 42364.668 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2O, KIAA1734 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9C0C9, (E3-independent) E2 ubiquitin-conjugating enzyme
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-P4K / polyethylene glycol / 3,6,9,12,15,18,21,24,27,30,33,36,39,42-tetradecaoxatetratetracontan-1-ol


Mass: 662.804 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H62O15 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Trimethylamine N-oxide dihydrate, 0.1 M Tris pH 8.5, 20% (w/v) Polyethylene glycol monomethyl ether 2,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.596→64 Å / Num. obs: 67712 / % possible obs: 100 % / Redundancy: 13.28 % / Biso Wilson estimate: 32.27 Å2 / CC1/2: 1 / Net I/σ(I): 17.44
Reflection shellResolution: 1.596→1.624 Å / Num. unique obs: 3358 / CC1/2: 0.1206

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
PHASERphasing
STARANISOdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.33 Å / SU ML: 0.1669 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.6091
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1916 2294 5.07 %
Rwork0.167 42990 -
obs0.1682 45284 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.32 Å2
Refinement stepCycle: LAST / Resolution: 1.8→49.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2877 0 77 192 3146
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01763031
X-RAY DIFFRACTIONf_angle_d1.49524071
X-RAY DIFFRACTIONf_chiral_restr0.1008438
X-RAY DIFFRACTIONf_plane_restr0.0132517
X-RAY DIFFRACTIONf_dihedral_angle_d16.59771183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.25551080.2421821X-RAY DIFFRACTION65.55
1.84-1.880.23161240.21652125X-RAY DIFFRACTION77.61
1.88-1.930.21941530.19192394X-RAY DIFFRACTION86.43
1.93-1.980.19061520.19082653X-RAY DIFFRACTION95.7
1.98-2.040.20531470.19332755X-RAY DIFFRACTION99.69
2.04-2.110.21081550.17332780X-RAY DIFFRACTION100
2.11-2.180.20481350.16372806X-RAY DIFFRACTION100
2.18-2.270.19241440.15452797X-RAY DIFFRACTION100
2.27-2.370.17321310.16192829X-RAY DIFFRACTION100
2.37-2.50.19651460.16132792X-RAY DIFFRACTION100
2.5-2.650.21761590.18252825X-RAY DIFFRACTION100
2.65-2.860.21281340.19162828X-RAY DIFFRACTION100
2.86-3.140.23541440.18362832X-RAY DIFFRACTION100
3.14-3.60.18681440.17022866X-RAY DIFFRACTION99.97
3.6-4.530.16431640.13992864X-RAY DIFFRACTION99.97
4.53-49.330.17411540.16053023X-RAY DIFFRACTION99.81
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)
13.873372628270.04454016145760.2743130128012.203587428560.2294668792972.69546036660.2821065415210.0420075955573-0.9345059177670.0795463289977-0.0641953849422-0.1131960631811.056704778050.51155561506-0.1879432435020.768908167850.185188898345-0.1293525386970.434929719093-0.05314826025960.64261766547820.8031283344-10.5059630857-5.57074631991
21.968372563590.03672624389371.267927645450.805580666874-0.1645487483343.022768242090.05181325661070.0647953846937-0.08315644231590.00463538578082-0.0457196572324-0.03278669781270.1040275738190.15683417648-0.0049987299170.2036298741470.01179597307830.04489227812490.1459895584370.01945235385380.24656055003416.93199709910.24271583991.20842949548
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'C' and (resid 1 through 76)CA1 - 761 - 76
22chain 'A' and (resid 927 through 1287)AB927 - 12871 - 283

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