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- PDB-9mc4: Cryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 4 -

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Basic information

Entry
Database: PDB / ID: 9mc4
TitleCryo-EM structure of Human UBA1-UBE2O-Ub -Transthiolation state 4
Components
  • (E3-independent) E2 ubiquitin-conjugating enzyme
  • Polyubiquitin-C
  • Ubiquitin-like modifier-activating enzyme 1
KeywordsCYTOSOLIC PROTEIN / cryo-EM / UBA1 / UBE2O / Ubiquitin
Function / homology
Function and homology information


E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / retrograde transport, endosome to Golgi / ubiquitin conjugating enzyme activity / protein monoubiquitination / protein K63-linked ubiquitination / Maturation of protein E / Maturation of protein E ...E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / (E3-independent) E2 ubiquitin-conjugating enzyme / positive regulation of BMP signaling pathway / retrograde transport, endosome to Golgi / ubiquitin conjugating enzyme activity / protein monoubiquitination / protein K63-linked ubiquitination / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / IRAK2 mediated activation of TAK1 complex / Prevention of phagosomal-lysosomal fusion / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Endosomal Sorting Complex Required For Transport (ESCRT) / Membrane binding and targetting of GAG proteins / Negative regulation of FLT3 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Constitutive Signaling by NOTCH1 HD Domain Mutants / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / 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 / Regulation of FZD by ubiquitination / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / 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 pyruvate metabolism / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Pexophagy / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / Regulation of BACH1 activity / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / 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) / Downregulation of TGF-beta receptor signaling / Josephin domain DUBs / Translesion synthesis by POLI / IKK complex recruitment mediated by RIP1 / Regulation of activated PAK-2p34 by proteasome mediated degradation / Gap-filling DNA repair synthesis and ligation in GG-NER / PINK1-PRKN Mediated Mitophagy / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / TCF dependent signaling in response to WNT / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Regulation of NF-kappa B signaling / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / activated TAK1 mediates p38 MAPK activation / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Regulation of signaling by CBL / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / NOTCH3 Activation and Transmission of Signal to the Nucleus / Negative regulators of DDX58/IFIH1 signaling / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Assembly of the pre-replicative complex / Deactivation of the beta-catenin transactivating complex / Vpu mediated degradation of CD4 / Stabilization of p53 / Negative regulation of FGFR2 signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of DVL / Negative regulation of FGFR4 signaling / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling / Degradation of AXIN / Regulation of TNFR1 signaling / EGFR downregulation / Termination of translesion DNA synthesis / Hh mutants are degraded by ERAD
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 / 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-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / 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
ADENOSINE MONOPHOSPHATE / Polyubiquitin-C / Ubiquitin-like modifier-activating enzyme 1 / (E3-independent) E2 ubiquitin-conjugating enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.32 Å
AuthorsChen, P.-T. / Wu, K.-P.
Funding support Taiwan, 2items
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 4
Authors: Chen, P.-T. / Wu, K.-P.
History
DepositionMar 17, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
A: Ubiquitin-like modifier-activating enzyme 1
B: (E3-independent) E2 ubiquitin-conjugating enzyme
C: Polyubiquitin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)268,5424
Polymers268,1953
Non-polymers3471
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Ubiquitin-like modifier-activating enzyme 1 / Protein A1S9 / Ubiquitin-activating enzyme E1


Mass: 117976.609 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA1, A1S9T, UBE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22314, E1 ubiquitin-activating enzyme
#2: Protein (E3-independent) E2 ubiquitin-conjugating enzyme / E2/E3 hybrid ubiquitin-protein ligase UBE2O / Ubiquitin carrier protein O / Ubiquitin-conjugating ...E2/E3 hybrid ubiquitin-protein ligase UBE2O / Ubiquitin carrier protein O / Ubiquitin-conjugating enzyme E2 O / Ubiquitin-conjugating enzyme E2 of 230 kDa / Ubiquitin-conjugating enzyme E2-230K / Ubiquitin-protein ligase O


Mass: 141554.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2O, KIAA1734 / Production host: Homo sapiens (human)
References: UniProt: Q9C0C9, (E3-independent) E2 ubiquitin-conjugating enzyme
#3: Protein Polyubiquitin-C


Mass: 8663.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0CG48
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The complex of human UBA1-UBE2O-Ub / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.6
SpecimenConc.: 1.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 113600 / Symmetry type: POINT

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