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- EMDB-53130: Consensus structure of dUBA1-UbDha-dBIRC6 trapped ternary complex -

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Basic information

Entry
Database: EMDB / ID: EMD-53130
TitleConsensus structure of dUBA1-UbDha-dBIRC6 trapped ternary complex
Map data
Sample
  • Complex: Trapped ternary complex with dUBA1 and dBIRC6 transferring ubiquitin
    • Protein or peptide: BIR repeat containing ubiquitin-conjugating enzyme, isoform B
    • Protein or peptide: E1 ubiquitin-activating enzyme
    • Protein or peptide: Polyubiquitin-C
  • Ligand: ADENOSINE MONOPHOSPHATE
KeywordsUbiquitin / E1 / E2 / Ligase / SIGNALING PROTEIN
Function / homology
Function and homology information


negative regulation of nurse cell apoptotic process / larval midgut cell programmed cell death / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ISG15 antiviral mechanism / Antigen processing: Ubiquitination & Proteasome degradation / mushroom body development / follicle cell of egg chamber development / regulation of Ras protein signal transduction / E1 ubiquitin-activating enzyme / regulation of programmed cell death ...negative regulation of nurse cell apoptotic process / larval midgut cell programmed cell death / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ISG15 antiviral mechanism / Antigen processing: Ubiquitination & Proteasome degradation / mushroom body development / follicle cell of egg chamber development / regulation of Ras protein signal transduction / E1 ubiquitin-activating enzyme / regulation of programmed cell death / ubiquitin activating enzyme activity / peptidase inhibitor activity / lipid storage / programmed cell death / regulation of growth / oogenesis / neuron remodeling / negative regulation of macroautophagy / ubiquitin conjugating enzyme activity / spermatid development / negative regulation of hippo signaling / mitophagy / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / 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 / 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 / Downregulation of ERBB4 signaling / Regulation of FZD by ubiquitination / 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 / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of pyruvate metabolism / NF-kB is activated and signals survival / Regulation of innate immune responses to cytosolic DNA / Downregulation of ERBB2:ERBB3 signaling / Pexophagy / NRIF signals cell death from the nucleus / VLDLR internalisation and degradation / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by REV1 / InlB-mediated entry of Listeria monocytogenes into host cell / Translesion synthesis by POLK / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Downregulation of TGF-beta receptor signaling / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / cellular response to starvation / 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 / regulation of cytokinesis / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of NF-kappa B signaling / Asymmetric localization of PCP proteins / activated TAK1 mediates p38 MAPK activation / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Regulation of signaling by CBL / Negative regulators of DDX58/IFIH1 signaling / Vpu mediated degradation of CD4 / NOTCH3 Activation and Transmission of Signal to the Nucleus / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A
Similarity search - Function
Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Baculoviral IAP repeat-containing protein 6 / Baculoviral IAP repeat-containing protein 6 / 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, conserved site / Ubiquitin-activating enzyme signature 1. / Baculoviral IAP repeat-containing protein 6 / Baculoviral IAP repeat-containing protein 6 / 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-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 / 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 / : / 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
Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6 / Polyubiquitin-C / E1 ubiquitin-activating enzyme
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.58 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: To Be Published
Title: Molecular basis of UBA6 specificity for ubiquitin E2 conjugating enzymes reveals a priority mechanism of BIRC6
Authors: Riechmann C / Ellison CJ / Anderson JW / Hofmann K / Sarkies P / Elliott PR
History
DepositionMar 13, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53130.png

Downloads & links

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Map

FileDownload / File: emd_53130.map.gz / Format: CCP4 / Size: 152.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 342 pix.
= 283.86 Å		0.83 Å/pix.
x 342 pix.
= 283.86 Å		0.83 Å/pix.
x 342 pix.
= 283.86 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.24731402 - 0.71259856
Average (Standard dev.)0.00034687575 (±0.018107826)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions342342342
Spacing342342342
CellA=B=C: 283.86 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53130_msk_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53130_half_map_1.map
Projections & Slices
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Histogram

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Half map: #1

Fileemd_53130_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Trapped ternary complex with dUBA1 and dBIRC6 transferring ubiquitin

EntireName: Trapped ternary complex with dUBA1 and dBIRC6 transferring ubiquitin
Components
  • Complex: Trapped ternary complex with dUBA1 and dBIRC6 transferring ubiquitin
    • Protein or peptide: BIR repeat containing ubiquitin-conjugating enzyme, isoform B
    • Protein or peptide: E1 ubiquitin-activating enzyme
    • Protein or peptide: Polyubiquitin-C
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: Trapped ternary complex with dUBA1 and dBIRC6 transferring ubiquitin

SupramoleculeName: Trapped ternary complex with dUBA1 and dBIRC6 transferring ubiquitin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 180 KDa

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Macromolecule #1: BIR repeat containing ubiquitin-conjugating enzyme, isoform B

MacromoleculeName: BIR repeat containing ubiquitin-conjugating enzyme, isoform B
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 35.56534 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPEPQSKSIE QRYLELMKKR QFDTFDMIVE SDNNSFRFVV SHHFEKMVRL AGDRYHPSRV KRLAQEAVTL STSLPLSFSS SVFVRCDTD RLDIMKVLIT GPADTPYANG CFEFDVFFPP DYPNQPMLIN LETTGRHSVR FNPNLYNDGK VCLSVLNTWH G RPEEKWNA ...String:
GPEPQSKSIE QRYLELMKKR QFDTFDMIVE SDNNSFRFVV SHHFEKMVRL AGDRYHPSRV KRLAQEAVTL STSLPLSFSS SVFVRCDTD RLDIMKVLIT GPADTPYANG CFEFDVFFPP DYPNQPMLIN LETTGRHSVR FNPNLYNDGK VCLSVLNTWH G RPEEKWNA QTSSFLQVLV SIQSLILVPE PYFNEPGFER SRGSPSGTNS SREYNSNIYQ ACVRWAMLEQ IRSPSQCFKD VI HKHFWLK REEICAQIEG WIEELGKPQY TERASRTISF NSMVLRRHYR HLREELSKLK PPRGLEDL

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

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Macromolecule #2: E1 ubiquitin-activating enzyme

MacromoleculeName: E1 ubiquitin-activating enzyme / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: E1 ubiquitin-activating enzyme
Source (natural)Organism: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 112.045164 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPMAGNSAAA GGDIDESLYS RQLYVLGHDA MRRMANSDIL LSGLGGLGLE IAKNVILGGV KSITLHDTAT CGLHDLSSQF YLTEADIGK NRAEASCAQL AELNNYVRTV SHTGPLTEEF LRKFRVVVLT NSDGEEQQRI AKFAHENGIA LIIAETRGLF A KVFCDFGE ...String:
GPMAGNSAAA GGDIDESLYS RQLYVLGHDA MRRMANSDIL LSGLGGLGLE IAKNVILGGV KSITLHDTAT CGLHDLSSQF YLTEADIGK NRAEASCAQL AELNNYVRTV SHTGPLTEEF LRKFRVVVLT NSDGEEQQRI AKFAHENGIA LIIAETRGLF A KVFCDFGE SFTIYDQDGT QPISTMIASI THDAQGVVTC LDETRHGFND GDYVTFSEVQ GMQELNGCQP LKITVLGPYT FS IGDTSKF GEYKSGGVAT QVKMPKTISF KPLAQATEEP EFLISDFAKL DSPATLHVAF NALSCYRKAH NGALPRPWNE EDA NSFLEV VRASSNAEVD EKLVLQFAKI CSGNTCPLDA AVGGIVAQEV LKACSGKFTP IYQWLYFDAL ECLPTEGVEE ADAQ PVGSR YDSQIAIFGK KFQEKLADSK WFIVGAGAIG CELLKNFGML GLGTGNGQIF VTDMDLIEKS NLNRQFLFRP HDVQK PKSM TAADAIKRMN PEVNVTAYEL RVGAETEKVF SEDFFGKLDG VANALDNVDA RIYMDRKCIF NRIPLVETGT LGTLGN VQV IVPFATESYS SSQDPPEKSI PICTLKNFPN AIEHTLQWAR DAFEGVFKQS AENAAQYIAD PQFTERIAKL PGIQPLE IL DSIKKALIDD KPKSFAHCVE WARLYWEDQY VNQIKQLLFN FPPDQITSSG QPFWSGPKRC PDPLVFDVND PMHLDFIY A AANLRAEVYG IEQVRNRETI AELVQKVKVP EFKPRSGVKI ETNEAAAAAS ANNFDDGELD QDRVDKIISE LLKNADKSS KITPLEFEKD DDSNLHMDFI VACSNLRAAN YKIPPADRHK SKLIAGKIIP AIATTTSVLS GLAVLEVIKL IVGHRDLVKF KNGFANLAL PFMAFSEPLP AAKNTYYGKE WTLWDRFEVT GELSLQEFLN YFEENEKLKI TMLSQGVSML YSFFMPKAKC S ERLPLPMS EVVRRVSKRR LEPHERSLVF EICCNDVDGE DVEVPYVRYT LP

UniProtKB: E1 ubiquitin-activating enzyme

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Macromolecule #3: Polyubiquitin-C

MacromoleculeName: Polyubiquitin-C / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 8.590856 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGA

UniProtKB: Polyubiquitin-C

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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: 7.5
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: 36.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.1 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: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 333479
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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