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- PDB-28mj: Cryo-EM structure of UBA6 in complex with FAT10 in the pre-adenyl... -

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Basic information

Entry
Database: PDB / ID: 28mj
TitleCryo-EM structure of UBA6 in complex with FAT10 in the pre-adenylation state.
Components
  • Ubiquitin D
  • Ubiquitin-like modifier-activating enzyme 6
KeywordsSIGNALING PROTEIN / Ubiquitin-activating enzyme / ubiquitin-like protein / adenylation / signalling cascade
Function / homology
Function and homology information


protein modification by small protein conjugation / FAT10 activating enzyme activity / aggresome assembly / myeloid dendritic cell differentiation / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / aggresome / regulation of mitotic cell cycle phase transition / proteasome binding / response to tumor necrosis factor ...protein modification by small protein conjugation / FAT10 activating enzyme activity / aggresome assembly / myeloid dendritic cell differentiation / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / aggresome / regulation of mitotic cell cycle phase transition / proteasome binding / response to tumor necrosis factor / Dengue Virus Attachment and Entry / response to type II interferon / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / Neddylation / ubiquitin-dependent protein catabolic process / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / positive regulation of apoptotic process / DNA damage response / proteolysis / nucleoplasm / metal ion binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin D / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily ...Ubiquitin D / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / INOSITOL HEXAKISPHOSPHATE / Ubiquitin-like modifier-activating enzyme 6 / Ubiquitin D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.77 Å
AuthorsEllison, C.J. / Dalietou, E.V. / Riechmann, C. / Elliott, P.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)APP19978 United Kingdom
Cancer Research UKDRCPFA-Jun24/100003 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Structural determinants for FAT10 activation and transfer from UBA6 to E2 enzymes.
Authors: Cara J Ellison / Carlos Riechmann / Evmorfia V Dalietou / Michael D R Simmons / Emma C Dodd / Paul R Elliott /
Abstract: Attachment of the ubiquitin-like protein (UBL) FAT10 onto substrates targets them for proteasomal degradation. Like ubiquitin, FAT10 is activated by the E1 enzyme UBA6 then transferred to E2 enzymes, ...Attachment of the ubiquitin-like protein (UBL) FAT10 onto substrates targets them for proteasomal degradation. Like ubiquitin, FAT10 is activated by the E1 enzyme UBA6 then transferred to E2 enzymes, but mechanisms controlling ubiquitin versus FAT10 activation by UBA6 and FAT10 transfer onto E2s remain unclear. Using cryo-EM, we visualise all stages of FAT10 E1-E2 handover: adenylation, thiolation and transthiolation. We find that FAT10 monopolises UBA6 by out-competing ubiquitin for thiolation and blocking the adenylation domain, preventing further UBL recruitment and promoting FAT10 signalling. We profiled UBA6-compatible E2 enzymes and found FAT10 transfer is restricted to a select subset associated with specific cellular pathways. UBE2Z (USE1) showed highest activity followed by UBE2D2, UBE2J2 and UBE2S. Capturing FAT10 or ubiquitin transfer from UBA6 to UBE2Z reveals UBE2Z is highly specialised for FAT10 transfer. It simultaneously engages both FAT10 domains (UBL1 and UBL2) and co-ordinates the metabolite inositol hexakisphosphate (InsP) bound within the UBA6 catalytic domain. This InsP co-ordination extends to other FAT10 compatible E2s. Together, our structural and biochemical analyses reveal regulatory mechanisms underpinning FAT10 activation and transfer. We define principles governing selective FAT10 transfer, highlighting favourable interactions with FAT10 C-terminal domain (UBL2) and stable UBA6 binding, ensuring controlled conjugation onto substrates.
History
DepositionFeb 7, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 23, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 23, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Ubiquitin D
A: Ubiquitin-like modifier-activating enzyme 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,0895
Polymers136,8982
Non-polymers1,1923
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Ubiquitin D / Diubiquitin / Ubiquitin-like protein FAT10


Mass: 18630.637 Da / Num. of mol.: 1 / Mutation: C7T, C9T, C134L, C160S, C162S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBD, FAT10 / Production host: Escherichia coli (E. coli) / References: UniProt: O15205
#2: Protein Ubiquitin-like modifier-activating enzyme 6 / Ubiquitin-activating enzyme 6 / Monocyte protein 4 / MOP-4 / Ubiquitin-activating enzyme E1-like ...Ubiquitin-activating enzyme 6 / Monocyte protein 4 / MOP-4 / Ubiquitin-activating enzyme E1-like protein 2 / E1-L2


Mass: 118266.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA6, MOP4, UBE1L2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0AVT1, E1 ubiquitin-activating enzyme
#3: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: UBA6 in complex with FAT10 in the pre-adenylation state.
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 42.2 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1crYOLOparticle selection
2cryoSPARCparticle selection
3PHENIX1.21.2_5419model refinement
14cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.77 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 795937 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 164.13 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00239536
ELECTRON MICROSCOPYf_angle_d0.532612936
ELECTRON MICROSCOPYf_chiral_restr0.04251470
ELECTRON MICROSCOPYf_plane_restr0.00331644
ELECTRON MICROSCOPYf_dihedral_angle_d6.14951329

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