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- EMDB-56645: Cryo-EM structure of UBA6-UbDha-UBE2Z trapped ternary complex (do... -

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Basic information

Entry
Database: EMDB / ID: EMD-56645
TitleCryo-EM structure of UBA6-UbDha-UBE2Z trapped ternary complex (doubly loaded)
Map data
Sample
  • Complex: UBA6-UbDha-UBE2Z trapped ternary complex (doubly loaded)
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 Z
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
    • Protein or peptide: Polyubiquitin-B
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsUbiquitin-activating enzyme / ubiquitin / adenylation / signalling cascade / SIGNALING PROTEIN
Function / homology
Function and homology information


FAT10 activating enzyme activity / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / mitochondrion transport along microtubule / positive regulation of protein monoubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Dengue Virus Attachment and Entry / Maturation of protein E ...FAT10 activating enzyme activity / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / mitochondrion transport along microtubule / positive regulation of protein monoubiquitination / E2 ubiquitin-conjugating enzyme / ubiquitin conjugating enzyme activity / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Dengue Virus Attachment and Entry / Maturation of protein E / Maturation of protein E / neuron projection morphogenesis / ER Quality Control Compartment (ERQC) / regulation of neuron apoptotic process / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / regulation of mitochondrial membrane potential / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Prevention of phagosomal-lysosomal fusion / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Negative regulation of FLT3 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Constitutive Signaling by NOTCH1 HD Domain Mutants / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1,TRAF6-dependent induction of TAK1 complex / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / Regulation of FZD by ubiquitination / p75NTR recruits signalling complexes / positive regulation of protein ubiquitination / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / regulation of proteasomal protein catabolic process / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / PD-L1(CD274) glycosylation and translocation to plasma membrane / NRIF signals cell death from the nucleus / Downregulation of ERBB2:ERBB3 signaling / Regulation of PTEN localization / Regulation of innate immune responses to cytosolic DNA / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / Regulation of BACH1 activity / InlB-mediated entry of Listeria monocytogenes into host cell / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLI / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Gap-filling DNA repair synthesis and ligation in GG-NER / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / Regulation of activated PAK-2p34 by proteasome mediated degradation / TCF dependent signaling in response to WNT / activated TAK1 mediates p38 MAPK activation / Regulation of NF-kappa B signaling / Maturation of DENV proteins / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / NOTCH3 Activation and Transmission of Signal to the Nucleus / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / Asymmetric localization of PCP proteins / Negative regulation of FGFR3 signaling / Ubiquitin-dependent degradation of Cyclin D / Peroxisomal protein import / Fanconi Anemia Pathway / SCF-beta-TrCP mediated degradation of Emi1 / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Stabilization of p53 / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Enterobacterial factors antagonize host defense / Negative regulation of FGFR1 signaling / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Termination of translesion DNA synthesis / Assembly of the pre-replicative complex
Similarity search - Function
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, 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 signature. / Ubiquitin conserved site / 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 / Polyubiquitin-B / Ubiquitin-conjugating enzyme E2 Z
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 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_56645.png

Downloads & links

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Map

FileDownload / File: emd_56645.map.gz / Format: CCP4 / Size: 142.1 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 334 pix.
= 283.9 Å		0.85 Å/pix.
x 334 pix.
= 283.9 Å		0.85 Å/pix.
x 334 pix.
= 283.9 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: 0.12
Minimum - Maximum-0.22913373 - 0.5998294
Average (Standard dev.)0.00013334544 (±0.015865214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions334334334
Spacing334334334
CellA=B=C: 283.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_56645_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_56645_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : UBA6-UbDha-UBE2Z trapped ternary complex (doubly loaded)

EntireName: UBA6-UbDha-UBE2Z trapped ternary complex (doubly loaded)
Components
  • Complex: UBA6-UbDha-UBE2Z trapped ternary complex (doubly loaded)
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 Z
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
    • Protein or peptide: Polyubiquitin-B
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: UBA6-UbDha-UBE2Z trapped ternary complex (doubly loaded)

SupramoleculeName: UBA6-UbDha-UBE2Z trapped ternary complex (doubly loaded)
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: 118.25082 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 IPFSTLKSFP 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: Polyubiquitin-B

MacromoleculeName: Polyubiquitin-B / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.590856 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGA

UniProtKB: Polyubiquitin-B

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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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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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: 40.1 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: 0.5 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: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 80561
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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