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- EMDB-66842: UBA6-BIRC6 UBC-UbT -

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Basic information

Entry
Database: EMDB / ID: EMD-66842
TitleUBA6-BIRC6 UBC-UbT
Map data
Sample
  • Complex: Cryo-EM structure of UBA6-BIRC6 UBC-UbT
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
    • Protein or peptide: Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6
    • Protein or peptide: Ubiquitin
KeywordsUbiquitin conjugating enzyme / UBA6 / BIRC6 / E2/E3 chimeric enzyme / inhibitor of apoptosis / LIGASE
Function / homology
Function and homology information


FAT10 activating enzyme activity / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / labyrinthine layer development / ALK mutants bind TKIs / (E3-independent) E2 ubiquitin-conjugating enzyme / Flemming body / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / ubiquitin conjugating enzyme activity ...FAT10 activating enzyme activity / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / labyrinthine layer development / ALK mutants bind TKIs / (E3-independent) E2 ubiquitin-conjugating enzyme / Flemming body / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / ubiquitin conjugating enzyme activity / Translation initiation complex formation / microtubule organizing center / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / cysteine-type endopeptidase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / 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 / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / 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 / 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 / p75NTR recruits signalling complexes / InlA-mediated entry of Listeria monocytogenes into host cells / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / NF-kB is activated and signals survival / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / Pexophagy / negative regulation of extrinsic apoptotic signaling pathway / Downregulation of ERBB2:ERBB3 signaling / Regulation of innate immune responses to cytosolic DNA / NRIF signals cell death from the nucleus / Regulation of PTEN localization / VLDLR internalisation and degradation / cytosolic ribosome / Activated NOTCH1 Transmits Signal to the Nucleus / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / 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 / regulation of cytokinesis / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / Translesion synthesis by POLI / 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 / trans-Golgi network / 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 / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Ubiquitin-dependent degradation of Cyclin D
Similarity search - Function
Baculoviral IAP repeat-containing protein 6 / Baculoviral IAP repeat-containing protein 6 / 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 ...Baculoviral IAP repeat-containing protein 6 / Baculoviral IAP repeat-containing protein 6 / 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 / BIR repeat / Inhibitor of Apoptosis domain / BIR repeat profile. / Baculoviral inhibition of apoptosis protein repeat / 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 / S27a-like superfamily / Ribosomal protein S27a / Ribosomal protein S27a / Ribosomal protein S27a / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc-binding ribosomal protein / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme 6 / Ubiquitin-ribosomal protein eS31 fusion protein / Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsTong ZT / Ai HS
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005, 92253302, 22227810, China
CitationJournal: To Be Published
Title: UBA6-BIRC6 UBC-UbT
Authors: Tong ZT / Ai HS
History
DepositionOct 30, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66842.png

Downloads & links

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Map

FileDownload / File: emd_66842.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 200 pix.
= 161.6 Å		0.81 Å/pix.
x 200 pix.
= 161.6 Å		0.81 Å/pix.
x 200 pix.
= 161.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.808 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015
Minimum - Maximum-0.12959926 - 0.15841125
Average (Standard dev.)0.000009437777 (±0.006140238)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 161.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66842_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_66842_additional_1.map
Projections & Slices
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Half map: #2

Fileemd_66842_half_map_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_66842_half_map_2.map
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Sample components

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Entire : Cryo-EM structure of UBA6-BIRC6 UBC-UbT

EntireName: Cryo-EM structure of UBA6-BIRC6 UBC-UbT
Components
  • Complex: Cryo-EM structure of UBA6-BIRC6 UBC-UbT
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
    • Protein or peptide: Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6
    • Protein or peptide: Ubiquitin

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Supramolecule #1: Cryo-EM structure of UBA6-BIRC6 UBC-UbT

SupramoleculeName: Cryo-EM structure of UBA6-BIRC6 UBC-UbT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #3, #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 162.3 kDa/nm

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Macromolecule #1: Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6

MacromoleculeName: Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: (E3-independent) E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.265973 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: VLKSLEEKYV AVMKKLQFDT FEMVSEDEDG KLGFKVNYHY MSQVKNANDA NSAARARRLA QEAVTLSTSL PLSSSSSVFV RCDEERLDI MKVLITGPAD TPYANGCFEF DVYFPQDYPS SPPLVNLETT GGHSVRFNPN LYNDGKVCLS ILNTWHGRPE E KWNPQTSS ...String:
VLKSLEEKYV AVMKKLQFDT FEMVSEDEDG KLGFKVNYHY MSQVKNANDA NSAARARRLA QEAVTLSTSL PLSSSSSVFV RCDEERLDI MKVLITGPAD TPYANGCFEF DVYFPQDYPS SPPLVNLETT GGHSVRFNPN LYNDGKVCLS ILNTWHGRPE E KWNPQTSS FLQVLVSVQS LILVAEPYFN EPGYERSRGT PSGTQSSREY DGNIRQATVK WAMLEQIRNP SPCFKEVIHK HF YLKRVEI MAQCEEWIAD IQQYSSDKRV GRTMSHHAAA LKRHTAQLRE ELLKLPCPEG LDPDTDDAPE VCRATTGAEE TLM HDQVKP SSSKELPSDF QL

UniProtKB: Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6

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Macromolecule #2: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.576831 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGG

UniProtKB: Ubiquitin-ribosomal protein eS31 fusion protein

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Macromolecule #3: Ubiquitin-like modifier-activating enzyme 6

MacromoleculeName: Ubiquitin-like modifier-activating enzyme 6 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: E1 ubiquitin-activating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.112727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEGSEPVAAH QGEEASCSSW GTGSTNKNLP IMSTASVEID DALYSRQRYV LGDTAMQKMA KSHVFLSGMG GLGLEIAKNL VLAGIKAVT IHDTEKCQAW DLGTNFFLSE DDVVNKRNRA EAVLKHIAEL NPYVHVTSSS VPFNETTDLS FLDKYQCVVL T EMKLPLQK ...String:
MEGSEPVAAH QGEEASCSSW GTGSTNKNLP IMSTASVEID DALYSRQRYV LGDTAMQKMA KSHVFLSGMG GLGLEIAKNL VLAGIKAVT IHDTEKCQAW DLGTNFFLSE DDVVNKRNRA EAVLKHIAEL NPYVHVTSSS VPFNETTDLS FLDKYQCVVL T EMKLPLQK KINDFCRSQC PPIKFISADV HGIWSRLFCD FGDEFEVLDT TGEEPKEIFI SNITQANPGI VTCLENHPHK LE TGQFLTF REINGMTGLN GSIQQITVIS PFSFSIGDTT ELEPYLHGGI AVQVKTPKTV FFESLERQLK HPKCLIVDFS NPE APLEIH TAMLALDQFQ EKYSRKPNVG CQQDSEELLK LATSISETLE EKPDVNADIV HWLSWTAQGF LSPLAAAVGG VASQ EVLKA VTGKFSPLCQ WLYLEAADIV ESLGKPECEE FLPRGDRYDA LRACIGDTLC QKLQNLNIFL VGCGAIGCEM LKNFA LLGV GTSKEKGMIT VTDPDLIEKS NLNRQFLFRP HHIQKPKSYT AADATLKINS QIKIDAHLNK VCPTTETIYN DEFYTK QDV IITALDNVEA RRYVDSRCLA NLRPLLDSGT MGTKGHTEVI VPHLTESYNS HRDPPEEEIP FCTLKSFPAA IEHTIQW AR DKFESSFSHK PSLFNKFWQT YSSAEEVLQK IQSGHSLEGC FQVIKLLSRR PRNWSQCVEL ARLKFEKYFN HKALQLLH C FPLDIRLKDG SLFWQSPKRP PSPIKFDLNE PLHLSFLQNA AKLYATVYCI PFAEEDLSAD ALLNILSEVK IQEFKPSNK VVQTDETARK PDHVPISSED ERNAIFQLEK AILSNEATKS DLQMAVLSFE KDDDHNGHID FITAASNLRA KMYSIEPADR FKTKRIAGK IIPAIATTTA TVSGLVALEM IKVTGGYPFE AYKNCFLNLA IPIVVFTETT EVRKTKIRNG ISFTIWDRWT V HGKEDFTL LDFINAVKEK YGIEPTMVVQ GVKMLYVPVM PGHAKRLKLT MHKLVKPTTE KKYVDLTVSF APDIDGDEDL PG PPVRYYF SHDTD

UniProtKB: Ubiquitin-like modifier-activating enzyme 6

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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: FEI FALCON IV (4k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 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
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 1201224
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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