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- EMDB-53188: Structure of UBA6 (cluster 3) -

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Basic information

Entry
Database: EMDB / ID: EMD-53188
TitleStructure of UBA6 (cluster 3)
Map data
Sample
  • Complex: UBA6
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsE1 / Ligase / SIGNALING PROTEIN
Function / homology
Function and homology information


FAT10 activating enzyme activity / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / ATP binding / nucleus ...FAT10 activating enzyme activity / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / 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 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / 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 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
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.99 Å
AuthorsRiechmann C / Elliott PR
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)BB/Y008936/1 United Kingdom
Cancer Research UKDRCPFA-Jun24/100003 United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: UBA6 specificity for ubiquitin E2 conjugating enzymes reveals a priority mechanism of BIRC6.
Authors: Carlos Riechmann / Cara J Ellison / Jake W Anderson / Kay Hofmann / Peter Sarkies / Paul R Elliott /
Abstract: In mammals, ubiquitylation is orchestrated by the canonical ubiquitin-activating E1 enzyme UBA1 and the orthogonal E1 UBA6. Growing evidence underscores the essentiality of both E1s, which ...In mammals, ubiquitylation is orchestrated by the canonical ubiquitin-activating E1 enzyme UBA1 and the orthogonal E1 UBA6. Growing evidence underscores the essentiality of both E1s, which differentiate between 29 active ubiquitin-conjugating enzymes (E2s). The mechanisms governing this distinction have remained unclear. Here we establish a framework for ubiquitin E1-E2 specificity. Focusing on UBA6-controlled ubiquitylation cascades, we reveal that BIRC6, a UBA6-exclusive E2, gains priority over all other UBA6-competent E2s, underpinning the functional importance of defined UBA6-BIRC6 ubiquitylation events in regulating cell death, embryogenesis and autophagy. By capturing BIRC6 receiving ubiquitin from UBA6 in different states, we observe BIRC6 engaging with the UBA6 ubiquitin fold domain, driving an exceptionally high-affinity interaction that is modulated by the UBA6 Cys-Cap loop. Using this interaction as a template, we demonstrate how to confer activity between E2s and their noncognate E1, providing a tool to delineate E1-E2-dependent pathways. Lastly, we explain how BIRC6 priority does not lead to inhibition of UBA6, through a bespoke thioester switch mechanism that disengages BIRC6 upon receiving ubiquitin. Our findings propose a concept of hierarchy of E2 activity with cognate E1s, which may explain how ubiquitin E1s can each function with over a dozen E2s and orchestrate E2-specific cellular functions.
History
DepositionMar 17, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53188.png

Downloads & links

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Map

FileDownload / File: emd_53188.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.24655658 - 0.67119473
Average (Standard dev.)-0.0012274089 (±0.025540646)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53188_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_53188_half_map_1.map
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Histogram

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Half map: #2

Fileemd_53188_half_map_2.map
Projections & Slices
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Sample components

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Entire : UBA6

EntireName: UBA6
Components
  • Complex: UBA6
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: UBA6

SupramoleculeName: UBA6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 120 KDa

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Macromolecule #1: Ubiquitin-like modifier-activating enzyme 6

MacromoleculeName: Ubiquitin-like modifier-activating enzyme 6 / type: protein_or_peptide / ID: 1 / 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 #2: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / 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: 37.45 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17392
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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