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- EMDB-63793: Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-63793
TitleCryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 1
Map data
Sample
  • Complex: The complex of human UBA1-UBE2O-Ub
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 1
    • Protein or peptide: (E3-independent) E2 ubiquitin-conjugating enzyme
    • Protein or peptide: Ubiquitin
  • Ligand: ADENOSINE MONOPHOSPHATE
Keywordscryo-EM / UBA1 / UBE2O / Ubiquitin / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / positive regulation of BMP signaling pathway / (E3-independent) E2 ubiquitin-conjugating enzyme / retrograde transport, endosome to Golgi / mitochondrion transport along microtubule / positive regulation of protein monoubiquitination / ubiquitin conjugating enzyme activity / protein monoubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator ...E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / positive regulation of BMP signaling pathway / (E3-independent) E2 ubiquitin-conjugating enzyme / retrograde transport, endosome to Golgi / mitochondrion transport along microtubule / positive regulation of protein monoubiquitination / ubiquitin conjugating enzyme activity / protein monoubiquitination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Dengue Virus Attachment and Entry / protein K63-linked ubiquitination / neuron projection morphogenesis / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / regulation of neuron apoptotic process / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / regulation of mitochondrial membrane potential / 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 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / 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 / 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 / positive regulation of protein ubiquitination / p75NTR recruits signalling complexes / 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 / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / 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 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / Regulation of BACH1 activity / Translesion synthesis by POLK / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / InlB-mediated entry of Listeria monocytogenes into host cell / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / 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 / Regulation of NF-kappa B signaling / activated TAK1 mediates p38 MAPK activation / 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 / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / 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 / NIK-->noncanonical NF-kB signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / Stabilization of p53 / TNFR2 non-canonical NF-kB pathway / Negative regulation of FGFR2 signaling / Enterobacterial factors antagonize host defense / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling
Similarity search - Function
: / : / : / UBE2O, ubiquitin binding SH3-C domain / UBE2O, N-terminal SH3-A domain / UBE2O, tandem tSH3-B domain / : / UBE2O, SH3-B domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. ...: / : / : / UBE2O, ubiquitin binding SH3-C domain / UBE2O, N-terminal SH3-A domain / UBE2O, tandem tSH3-B domain / : / UBE2O, SH3-B domain / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / 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, Cys active site / Ubiquitin-activating enzyme active site. / 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
Polyubiquitin-B / Ubiquitin-like modifier-activating enzyme 1 / (E3-independent) E2 ubiquitin-conjugating enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsChen P-T / Wu K-P
Funding support Taiwan, 2 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan)AS-CDA-110-L03 Taiwan
Academia Sinica (Taiwan)AS-GCS-113-L05 Taiwan
CitationJournal: To Be Published
Title: Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 1
Authors: Chen P-T / Wu K-P
History
DepositionMar 17, 2025-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63793.png

Downloads & links

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Map

FileDownload / File: emd_63793.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 432 pix.
= 279.936 Å		0.65 Å/pix.
x 432 pix.
= 279.936 Å		0.65 Å/pix.
x 432 pix.
= 279.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.20793927 - 0.3904048
Average (Standard dev.)-0.00036855854 (±0.007616608)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 279.936 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_63793_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63793_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of human UBA1-UBE2O-Ub

EntireName: The complex of human UBA1-UBE2O-Ub
Components
  • Complex: The complex of human UBA1-UBE2O-Ub
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 1
    • Protein or peptide: (E3-independent) E2 ubiquitin-conjugating enzyme
    • Protein or peptide: Ubiquitin
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: The complex of human UBA1-UBE2O-Ub

SupramoleculeName: The complex of human UBA1-UBE2O-Ub / 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 1

MacromoleculeName: Ubiquitin-like modifier-activating enzyme 1 / 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: 117.976609 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSSSPLSKKR RVSGPDPKPG SNCSPAQSVL SEVPSVPTNG MAKNGSEADI DEGLYSRQLY VLGHEAMKRL QTSSVLVSGL RGLGVEIAK NIILGGVKAV TLHDQGTAQW ADLSSQFYLR EEDIGKNRAE VSQPRLAELN SYVPVTAYTG PLVEDFLSGF Q VVVLTNTP ...String:
MSSSPLSKKR RVSGPDPKPG SNCSPAQSVL SEVPSVPTNG MAKNGSEADI DEGLYSRQLY VLGHEAMKRL QTSSVLVSGL RGLGVEIAK NIILGGVKAV TLHDQGTAQW ADLSSQFYLR EEDIGKNRAE VSQPRLAELN SYVPVTAYTG PLVEDFLSGF Q VVVLTNTP LEDQLRVGEF CHNRGIKLVV ADTRGLFGQL FCDFGEEMIL TDSNGEQPLS AMVSMVTKDN PGVVTCLDEA RH GFESGDF VSFSEVQGMV ELNGNQPMEI KVLGPYTFSI CDTSNFSDYI RGGIVSQVKV PKKISFKSLV ASLAEPDFVV TDF AKFSRP AQLHIGFQAL HQFCAQHGRP PRPRNEEDAA ELVALAQAVN ARALPAVQQN NLDEDLIRKL AYVAAGDLAP INAF IGGLA AQEVMKACSG KFMPIMQWLY FDALECLPED KEVLTEDKCL QRQNRYDGQV AVFGSDLQEK LGKQKYFLVG AGAIG CELL KNFAMIGLGC GEGGEIIVTD MDTIEKSNLN RQFLFRPWDV TKLKSDTAAA AVRQMNPHIR VTSHQNRVGP DTERIY DDD FFQNLDGVAN ALDNVDARMY MDRRCVYYRK PLLESGTLGT KGNVQVVIPF LTESYSSSQD PPEKSIPICT LKNFPNA IE HTLQWARDEF EGLFKQPAEN VNQYLTDPKF VERTLRLAGT QPLEVLEAVQ RSLVLQRPQT WADCVTWACH HWHTQYSN N IRQLLHNFPP DQLTSSGAPF WSGPKRCPHP LTFDVNNPLH LDYVMAAANL FAQTYGLTGS QDRAAVATFL QSVQVPEFT PKSGVKIHVS DQELQSANAS VDDSRLEELK ATLPSPDKLP GFKMYPIDFE KDDDSNFHMD FIVAASNLRA ENYDIPSADR HKSKLIAGK IIPAIATTTA AVVGLVCLEL YKVVQGHRQL DSYKNGFLNL ALPFFGFSEP LAAPRHQYYN QEWTLWDRFE V QGLQPNGE EMTLKQFLDY FKTEHKLEIT MLSQGVSMLY SFFMPAAKLK ERLDQPMTEI VSRVSKRKLG RHVRALVLEL CC NDESGED VEVPYVRYTI R

UniProtKB: Ubiquitin-like modifier-activating enzyme 1

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Macromolecule #2: (E3-independent) E2 ubiquitin-conjugating enzyme

MacromoleculeName: (E3-independent) E2 ubiquitin-conjugating enzyme / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: (E3-independent) E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 40.411566 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: VFSVLEFAPS NHSFKKIEFQ PPEAKKFFST VRKEMALLAT SLPEGIMVKT FEDRMDLFSA LIKGPTRTPY EDGLYLFDIQ LPNIYPAVP PHFCYLSQCS GRLNPNLYDN GKVCVSLLGT WIGKGTERWT SKSSLLQVLI SIQGLILVNE PYYNEAGFDS D RGLQEGYE ...String:
VFSVLEFAPS NHSFKKIEFQ PPEAKKFFST VRKEMALLAT SLPEGIMVKT FEDRMDLFSA LIKGPTRTPY EDGLYLFDIQ LPNIYPAVP PHFCYLSQCS GRLNPNLYDN GKVCVSLLGT WIGKGTERWT SKSSLLQVLI SIQGLILVNE PYYNEAGFDS D RGLQEGYE NSRCYNEMAL IRVVQSMTQL VRRPPEVFEQ EIRQHFSTGG WRLVNRIESW LETHALLEKA QALPNGVPKA SS SPEPPAV AELSDSGQQE PEDGGPAPGE ASQGSDSEGG AQGLASASRD HTDQTSETAP DASVPPSVKP KKRRKSYRSF LPE KSGYPD IGFPLFPLSK GFIKSIRGVL TQFRAALLEA GMPECTEDK

UniProtKB: (E3-independent) E2 ubiquitin-conjugating enzyme

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Macromolecule #3: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Polyubiquitin-B

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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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.6
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold3
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 69286
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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