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- EMDB-73059: Cryo-EM structure of double-loaded human UBA6-UBE2Z-FAT10(t)/FAT1... -

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Entry
Database: EMDB / ID: EMD-73059
TitleCryo-EM structure of double-loaded human UBA6-UBE2Z-FAT10(t)/FAT10(a) thioester mimetic complex.
Map datastructure of double-loaded human UBA6-UBE2Z-FAT10(t)/FAT10(a) thioester mimetic complex.
Sample
  • Complex: Complex
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 Z
    • Protein or peptide: Ubiquitin D
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: PYROPHOSPHATE 2-
KeywordsE1 E2 enzymes / TRANSFERASE / TRANSFERASE-Ligase complex
Function / homology
Function and homology information


FAT10 activating enzyme activity / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / E2 ubiquitin-conjugating enzyme / proteasome binding / response to stress / ubiquitin conjugating enzyme activity / response to tumor necrosis factor / Dengue Virus Attachment and Entry / Synthesis of active ubiquitin: roles of E1 and E2 enzymes ...FAT10 activating enzyme activity / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / E2 ubiquitin-conjugating enzyme / proteasome binding / response to stress / ubiquitin conjugating enzyme activity / response to tumor necrosis factor / Dengue Virus Attachment and Entry / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / molecular adaptor activity / protein ubiquitination / positive regulation of apoptotic process / apoptotic process / negative regulation of apoptotic process / DNA damage response / nucleoplasm / ATP binding / metal ion 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 D / Ubiquitin-like modifier-activating enzyme 6 / Ubiquitin-conjugating enzyme E2 Z
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsJia L / Ruben EA / Nayak D / Bury PS / Nayak A / Wasmuth EV / Olsen SK
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structures of UBA6 reveal mechanisms of E1-E2 specificity and dual FAT10/ubiquitin thioester transfer.
Authors: Digant Nayak / Lijia Jia / Priscila Dos Santos Bury / Eliza A Ruben / Ankita Shukla / Anindita Nayak / Caleb M Stratton / Pirouz Ebadi / Hee Cho / Anna A Tumanova / Joyce T Varughese / ...Authors: Digant Nayak / Lijia Jia / Priscila Dos Santos Bury / Eliza A Ruben / Ankita Shukla / Anindita Nayak / Caleb M Stratton / Pirouz Ebadi / Hee Cho / Anna A Tumanova / Joyce T Varughese / Lingmin Yuan / Fei Gao / Kristin E Cano / Christopher Davies / Patrick Sung / Michaela U Gack / Elizabeth V Wasmuth / Shaun K Olsen /
Abstract: UBA1 and UBA6 define parallel ubiquitin (Ub) activation systems that perform non-overlapping roles in Ub and ubiquitin-like protein (Ubl) signaling. Whereas UBA1 supports the canonical Ub pathway, ...UBA1 and UBA6 define parallel ubiquitin (Ub) activation systems that perform non-overlapping roles in Ub and ubiquitin-like protein (Ubl) signaling. Whereas UBA1 supports the canonical Ub pathway, UBA6 also activates the Ubl FAT10, linking Ub signaling to immune-regulated proteostasis. In addition to selective Ub/Ubl activation, UBA1 and UBA6 engage distinct sets of E2s, yet how these enzymes achieve selective E2 engagement has remained unclear. Using chemical trapping and high-resolution cryo-EM, we determine four structures of UBA6-E2 complexes representing the thioester-transfer step with either FAT10 or Ub, revealing how this E1 distinguishes its cognate partners. UBA6 achieves E2 specificity through coordinated contributions of the UFD and SCCH domains, a dual-domain mechanism that contrasts with the UFD-dominated selectivity of UBA1. The structures further show that an existing inositol hexakisphosphate (InsP₆)-binding site, unique to UBA6, stabilizes an expanded SCCH cleft that pre-organizes the enzyme for selective engagement of UBA6-specific E2s. These findings define principles for E1-E2 recognition and identify InsP₆ as a cofactor shaping specificity within the Ub-like conjugation network.
History
DepositionOct 7, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73059.png

Downloads & links

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Map

FileDownload / File: emd_73059.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of double-loaded human UBA6-UBE2Z-FAT10(t)/FAT10(a) thioester mimetic complex.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 213.248 Å		0.83 Å/pix.
x 256 pix.
= 213.248 Å		0.83 Å/pix.
x 256 pix.
= 213.248 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.167
Minimum - Maximum-1.2216172 - 1.8491637
Average (Standard dev.)-0.00021795886 (±0.055068478)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 213.248 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73059_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Additional map: Additional Map

Fileemd_73059_additional_1.map
AnnotationAdditional Map
Projections & Slices
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Histogram

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Half map: Half Map A

Fileemd_73059_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_73059_half_map_2.map
AnnotationHalf Map B
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Complex

EntireName: Complex
Components
  • Complex: Complex
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
    • Protein or peptide: Ubiquitin-conjugating enzyme E2 Z
    • Protein or peptide: Ubiquitin D
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: PYROPHOSPHATE 2-

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Supramolecule #1: Complex

SupramoleculeName: Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

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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: 114.475867 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: VEIDDALYSR QRYVLGDTAM QKMAKSHVFL SGMGGLGLEI AKNLVLAGIK AVTIHDTEKC QAWDLGTNFF LSEDDVVNKR NRAEAVLKH IAELNPYVHV TSSSVPFNET TDLSFLDKYQ CVVLTEMKLP LQKKINDFCR SQCPPIKFIS ADVHGIWSRL F CDFGDEFE ...String:
VEIDDALYSR QRYVLGDTAM QKMAKSHVFL SGMGGLGLEI AKNLVLAGIK AVTIHDTEKC QAWDLGTNFF LSEDDVVNKR NRAEAVLKH IAELNPYVHV TSSSVPFNET TDLSFLDKYQ CVVLTEMKLP LQKKINDFCR SQCPPIKFIS ADVHGIWSRL F CDFGDEFE VLDTTGEEPK EIFISNITQA NPGIVTCLEN HPHKLETGQF LTFREINGMT GLNGSIQQIT VISPFSFSIG DT TELEPYL HGGIAVQVKT PKTVFFESLE RQLKHPKCLI VDFSNPEAPL EIHTAMLALD QFQEKYSRKP NVGCQQDSEE LLK LATSIS ETLEEKPDVN ADIVHWLSWT AQGFLSPLAA AVGGVASQEV LKAVTGKFSP LCQWLYLEAA DIVESLGKPE CEEF LPRGD RYDALRACIG DTLCQKLQNL NIFLVGCGAI GCEMLKNFAL LGVGTSKEKG MITVTDPDLI EKSNLNRQFL FRPHH IQKP KSYTAADATL KINSQIKIDA HLNKVCPTTE TIYNDEFYTK QDVIITALDN VEARRYVDSR CLANLRPLLD SGTMGT KGH TEVIVPHLTE SYNSHRDPPE EEIPFCTLKS FPAAIEHTIQ WARDKFESSF SHKPSLFNKF WQTYSSAEEV LQKIQSG HS LEGCFQVIKL LSRRPRNWSQ CVELARLKFE KYFNHKALQL LHCFPLDIRL KDGSLFWQSP KRPPSPIKFD LNEPLHLS F LQNAAKLYAT VYCIPFAEED LSADALLNIL SEVKIQEFKP SNKVVQTDET ARKPDHVPIS SEDERNAIFQ LEKAILSNE ATKSDLQMAV LSFEKDDDHN GHIDFITAAS NLRAKMYSIE PADRFKTKRI AGKIIPAIAT TTATVSGLVA LEMIKVTGGY PFEAYKNCF LNLAIPIVVF TETTEVRKTK IRNGISFTIW DRWTVHGKED FTLLDFINAV KEKYGIEPTM VVQGVKMLYV P VMPGHAKR LKLTMHKLVK PTTEKKYVDL TVSFAPDIDG DEDLPGPPVR YYFSHDTD

UniProtKB: Ubiquitin-like modifier-activating enzyme 6

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Macromolecule #2: Ubiquitin-conjugating enzyme E2 Z

MacromoleculeName: Ubiquitin-conjugating enzyme E2 Z / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.96501 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GERTAPQSLL RIKRDIMSIY KEPPPGMFVV PDTVDMTRIH ALITGPFDTP YEGGFFLFVF RCPPDYPIHP PRVRLMTTGN NTVRFNPNF KRNGRVCLSI LGTWTGPAWS PAQSISSVLI SIQSLMTENP YHNEPGFEQE RHPGDSKNYN ECIRHETIRV A VCDMMEGK ...String:
GERTAPQSLL RIKRDIMSIY KEPPPGMFVV PDTVDMTRIH ALITGPFDTP YEGGFFLFVF RCPPDYPIHP PRVRLMTTGN NTVRFNPNF KRNGRVCLSI LGTWTGPAWS PAQSISSVLI SIQSLMTENP YHNEPGFEQE RHPGDSKNYN ECIRHETIRV A VCDMMEGK SPSPEPLRGV MEKSFLEYYD FYEVACKDRL HLQGQTMQDP FGEKRGHFDY QSLLMRLGLI RQKVLERLHN EN AEMDSDS SSSGTETDLH GSLRV

UniProtKB: Ubiquitin-conjugating enzyme E2 Z

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Macromolecule #3: Ubiquitin D

MacromoleculeName: Ubiquitin D / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.476471 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAPNASTLTV HVRSEEWDLM TFDANPYDSV KKIKEHVRSK TKVPVQDQVL LLGSKILKPR RSLSSYGIDK EKTIHLTLKV VKPSDEELP LFLVESGDEA KRHLLQVRRS SSVAQVKAMI ETKTGIIPET QIVTLNGKRL EDGKMMADYG IRKGNLLFLA S YSIGG

UniProtKB: Ubiquitin D

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Macromolecule #4: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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Macromolecule #5: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #6: PYROPHOSPHATE 2-

MacromoleculeName: PYROPHOSPHATE 2- / type: ligand / ID: 6 / Number of copies: 1 / Formula: POP
Molecular weightTheoretical: 175.959 Da
Chemical component information

ChemComp-POP:
PYROPHOSPHATE 2-

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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 (6k x 4k) / Average electron dose: 80.0 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: 1.2 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:

7sol

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 299646
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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