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- EMDB-56646: Cryo-EM structure of UBA6-FAT10Dha-UBE2Z trapped ternary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-56646
TitleCryo-EM structure of UBA6-FAT10Dha-UBE2Z trapped ternary complex
Map data
Sample
  • Complex: UBA6-FAT10Dha-UBE2Z trapped ternary complex
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 Z
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
    • Protein or peptide: Ubiquitin D
  • Ligand: INOSITOL HEXAKISPHOSPHATE
KeywordsUbiquitin-activating enzyme / ubiquitin-like protein / adenylation / signalling cascade / SIGNALING PROTEIN
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 / E2 ubiquitin-conjugating enzyme / regulation of mitotic cell cycle phase transition / proteasome binding ...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 / E2 ubiquitin-conjugating enzyme / regulation of mitotic cell cycle phase transition / proteasome binding / ubiquitin conjugating enzyme activity / 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 / molecular adaptor activity / positive regulation of canonical NF-kappaB signal transduction / protein ubiquitination / positive regulation of apoptotic process / apoptotic process / DNA damage response / negative regulation of apoptotic process / 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-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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme 6 / Ubiquitin D / Ubiquitin-conjugating enzyme E2 Z
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsEllison CJ / Riechmann C / Elliott PR
Funding support United Kingdom, 2 items
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 8, 2026-
Header (metadata) releaseSep 23, 2026-
Map releaseSep 23, 2026-
UpdateSep 23, 2026-
Current statusSep 23, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56646.png

Downloads & links

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Map

FileDownload / File: emd_56646.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 384 pix.
= 326.4 Å		0.85 Å/pix.
x 384 pix.
= 326.4 Å		0.85 Å/pix.
x 384 pix.
= 326.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.09332518 - 0.20911355
Average (Standard dev.)0.000118038086 (±0.0042335615)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 326.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_56646_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_56646_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : UBA6-FAT10Dha-UBE2Z trapped ternary complex

EntireName: UBA6-FAT10Dha-UBE2Z trapped ternary complex
Components
  • Complex: UBA6-FAT10Dha-UBE2Z trapped ternary complex
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 Z
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
    • Protein or peptide: Ubiquitin D
  • Ligand: INOSITOL HEXAKISPHOSPHATE

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Supramolecule #1: UBA6-FAT10Dha-UBE2Z trapped ternary complex

SupramoleculeName: UBA6-FAT10Dha-UBE2Z trapped ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Ubiquitin-conjugating enzyme E2 Z

MacromoleculeName: Ubiquitin-conjugating enzyme E2 Z / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.40325 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GPMAESPTEE AATAGAGAAG PGASSVAGVV GVSGSGGGFG PPFLPDVWAA AAAAGGAGGP GSGLAPLPGL PPSAAAHGAA LLSHWDPTL SSDWDGERTA PQCLLRIKRD IMSIYKEPPP GMFVVPDTVD MTKIHALITG PFDTPYEGGF FLFVFRCPPD Y PIHPPRVK ...String:
GPMAESPTEE AATAGAGAAG PGASSVAGVV GVSGSGGGFG PPFLPDVWAA AAAAGGAGGP GSGLAPLPGL PPSAAAHGAA LLSHWDPTL SSDWDGERTA PQCLLRIKRD IMSIYKEPPP GMFVVPDTVD MTKIHALITG PFDTPYEGGF FLFVFRCPPD Y PIHPPRVK LMTTGNNTVR FNPNFYRNGK VCLSILGTWT GPAWSPAQSI SSVLISIQSL MTENPYHNEP GFEQERHPGD SK NYNECIR HETIRVAVCD MMEGKCPCPE PLRGVMEKSF LEYYDFYEVA CKDRLHLQGQ TMQDPFGEKR GHFDYQSLLM RLG LIRQKV LERLHNENAE MDSDSSSSGT ETDLHGSLRV

UniProtKB: Ubiquitin-conjugating enzyme E2 Z

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Macromolecule #2: Ubiquitin-like modifier-activating enzyme 6

MacromoleculeName: Ubiquitin-like modifier-activating enzyme 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: E1 ubiquitin-activating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.266883 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPMEGSEPVA AHQGEEASCS SWGTGSTNKN LPIMSTASVE IDDALYSRQR YVLGDTAMQK MAKSHVFLSG MGGLGLEIAK NLVLAGIKA VTIHDTEKCQ AWDLGTNFFL SEDDVVNKRN RAEAVLKHIA ELNPYVHVTS SSVPFNETTD LSFLDKYQCV V LTEMKLPL ...String:
GPMEGSEPVA AHQGEEASCS SWGTGSTNKN LPIMSTASVE IDDALYSRQR YVLGDTAMQK MAKSHVFLSG MGGLGLEIAK NLVLAGIKA VTIHDTEKCQ AWDLGTNFFL SEDDVVNKRN RAEAVLKHIA ELNPYVHVTS SSVPFNETTD LSFLDKYQCV V LTEMKLPL QKKINDFCRS QCPPIKFISA DVHGIWSRLF CDFGDEFEVL DTTGEEPKEI FISNITQANP GIVTCLENHP HK LETGQFL TFREINGMTG LNGSIQQITV ISPFSFSIGD TTELEPYLHG GIAVQVKTPK TVFFESLERQ LKHPKCLIVD FSN PEAPLE IHTAMLALDQ FQEKYSRKPN VGCQQDSEEL LKLATSISET LEEKPDVNAD IVHWLSWTAQ GFLSPLAAAV GGVA SQEVL KAVTGKFSPL CQWLYLEAAD IVESLGKPEC EEFLPRGDRY DALRACIGDT LCQKLQNLNI FLVGCGAIGC EMLKN FALL GVGTSKEKGM ITVTDPDLIE KSNLNRQFLF RPHHIQKPKS YTAADATLKI NSQIKIDAHL NKVCPTTETI YNDEFY TKQ DVIITALDNV EARRYVDSRC LANLRPLLDS GTMGTKGHTE VIVPHLTESY NSHRDPPEEE IPFCTLKSFP AAIEHTI QW ARDKFESSFS HKPSLFNKFW QTYSSAEEVL QKIQSGHSLE GCFQVIKLLS RRPRNWSQCV ELARLKFEKY FNHKALQL L HCFPLDIRLK DGSLFWQSPK RPPSPIKFDL NEPLHLSFLQ NAAKLYATVY CIPFAEEDLS ADALLNILSE VKIQEFKPS NKVVQTDETA RKPDHVPISS EDERNAIFQL EKAILSNEAT KSDLQMAVLS FEKDDDHNGH IDFITAASNL RAKMYSIEPA DRFKTKRIA GKIIPAIATT TATVSGLVAL EMIKVTGGYP FEAYKNCFLN LAIPIVVFTE TTEVRKTKIR NGISFTIWDR W TVHGKEDF TLLDFINAVK EKYGIEPTMV VQGVKMLYVP VMPGHAKRLK LTMHKLVKPT TEKKYVDLTV SFAPDIDGDE DL PGPPVRY YFSHDTD

UniProtKB: Ubiquitin-like modifier-activating enzyme 6

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Macromolecule #3: Ubiquitin D

MacromoleculeName: Ubiquitin D / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.644664 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GPMAPNASTL TVHVRSEEWD LMTFDANPYD SVKKIKEHVR SKTKVPVQDQ VLLLGSKILK PRRSLSSYGI DKEKTIHLTL KVVKPSDEE LPLFLVESGD EAKRHLLQVR RSSSVAQVKA MIETKTGIIP ETQIVTLNGK RLEDGKMMAD YGIRKGNLLF L ASYSIGA

UniProtKB: Ubiquitin D

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Macromolecule #4: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 42.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9qic

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 233302
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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