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- EMDB-53155: Consensus structure of UBA6-UbDha-BIRC6 trapped ternary complex (... -

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Basic information

Entry
Database: EMDB / ID: EMD-53155
TitleConsensus structure of UBA6-UbDha-BIRC6 trapped ternary complex (doubly loaded)
Map data
Sample
  • Complex: Trapped ternary complex of BIRC6 with UBA6
    • Protein or peptide: Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
    • Protein or peptide: Polyubiquitin-C
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ADENOSINE MONOPHOSPHATE
KeywordsUbiquitin / E1 / E2 / Ligase / SIGNALING PROTEIN
Function / homology
Function and homology information


FAT10 activating enzyme activity / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / labyrinthine layer development / (E3-independent) E2 ubiquitin-conjugating enzyme / ALK mutants bind TKIs / Flemming body / ubiquitin conjugating enzyme activity / microtubule organizing center / cysteine-type endopeptidase inhibitor activity ...FAT10 activating enzyme activity / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / labyrinthine layer development / (E3-independent) E2 ubiquitin-conjugating enzyme / ALK mutants bind TKIs / Flemming body / ubiquitin conjugating enzyme activity / microtubule organizing center / cysteine-type endopeptidase inhibitor activity / 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 / 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 / negative regulation of extrinsic apoptotic signaling pathway / 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 / Degradation of DVL / Negative regulation of FGFR3 signaling / Fanconi Anemia Pathway / Peroxisomal protein import / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Negative regulation of FGFR2 signaling / Stabilization of p53 / Negative regulation of FGFR4 signaling / Degradation of AXIN / Downregulation of SMAD2/3:SMAD4 transcriptional activity / Negative regulation of FGFR1 signaling
Similarity search - Function
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 ...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/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
Ubiquitin-like modifier-activating enzyme 6 / Polyubiquitin-C / Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.09 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 14, 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_53155.png

Downloads & links

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Map

FileDownload / File: emd_53155.map.gz / Format: CCP4 / Size: 142.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 334 pix.
= 283.9 Å		0.85 Å/pix.
x 334 pix.
= 283.9 Å		0.85 Å/pix.
x 334 pix.
= 283.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.21972658 - 0.5576764
Average (Standard dev.)0.00065274566 (±0.015777474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions334334334
Spacing334334334
CellA=B=C: 283.9 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53155_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53155_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53155_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : Trapped ternary complex of BIRC6 with UBA6

EntireName: Trapped ternary complex of BIRC6 with UBA6
Components
  • Complex: Trapped ternary complex of BIRC6 with UBA6
    • Protein or peptide: Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
    • Protein or peptide: Polyubiquitin-C
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: Trapped ternary complex of BIRC6 with UBA6

SupramoleculeName: Trapped ternary complex of BIRC6 with UBA6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 170 KDa

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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: 36.834668 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: GPANQEKKLG EYSKKAAMKP KPLSVLKSLE EKYVAVMKKL QFDTFEMVSE DEDGKLGFKV NYHYMSQVKN ANDANSAARA RRLAQEAVT LSTSLPLSSS SSVFVRCDEE RLDIMKVLIT GPADTPYANG CFEFDVYFPQ DYPSSPPLVN LETTGGHSVR F NPNLYNDG ...String:
GPANQEKKLG EYSKKAAMKP KPLSVLKSLE EKYVAVMKKL QFDTFEMVSE DEDGKLGFKV NYHYMSQVKN ANDANSAARA RRLAQEAVT LSTSLPLSSS SSVFVRCDEE RLDIMKVLIT GPADTPYANG CFEFDVYFPQ DYPSSPPLVN LETTGGHSVR F NPNLYNDG KVCLSILNTW HGRPEEKWNP QTSSFLQVLV SVQSLILVAE PYFNEPGYER SRGTPSGTQS SREYDGNIRQ AT VKWAMLE QIRNPSPCFK EVIHKHFYLK RVEIMAQCEE WIADIQQYSS DKRVGRTMSH HAAALKRHTA QLREELLKLP CPE GLDPD

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

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Macromolecule #2: Ubiquitin-like modifier-activating enzyme 6

MacromoleculeName: Ubiquitin-like modifier-activating enzyme 6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: E1 ubiquitin-activating enzyme
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 118.25082 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPMEGSEPVA AHQGEEASCS SWGTGSTNKN LPIMSTASVE IDDALYSRQR YVLGDTAMQK MAKSHVFLSG MGGLGLEIAK NLVLAGIKA VTIHDTEKCQ AWDLGTNFFL SEDDVVNKRN RAEAVLKHIA ELNPYVHVTS SSVPFNETTD LSFLDKYQCV V LTEMKLPL ...String:
GPMEGSEPVA AHQGEEASCS SWGTGSTNKN LPIMSTASVE IDDALYSRQR YVLGDTAMQK MAKSHVFLSG MGGLGLEIAK NLVLAGIKA VTIHDTEKCQ AWDLGTNFFL SEDDVVNKRN RAEAVLKHIA ELNPYVHVTS SSVPFNETTD LSFLDKYQCV V LTEMKLPL QKKINDFCRS QCPPIKFISA DVHGIWSRLF CDFGDEFEVL DTTGEEPKEI FISNITQANP GIVTCLENHP HK LETGQFL TFREINGMTG LNGSIQQITV ISPFSFSIGD TTELEPYLHG GIAVQVKTPK TVFFESLERQ LKHPKCLIVD FSN PEAPLE IHTAMLALDQ FQEKYSRKPN VGCQQDSEEL LKLATSISET LEEKPDVNAD IVHWLSWTAQ GFLSPLAAAV GGVA SQEVL KAVTGKFSPL CQWLYLEAAD IVESLGKPEC EEFLPRGDRY DALRACIGDT LCQKLQNLNI FLVGCGAIGC EMLKN FALL GVGTSKEKGM ITVTDPDLIE KSNLNRQFLF RPHHIQKPKS YTAADATLKI NSQIKIDAHL NKVCPTTETI YNDEFY TKQ DVIITALDNV EARRYVDSRC LANLRPLLDS GTMGTKGHTE VIVPHLTESY NSHRDPPEEE IPFSTLKSFP AAIEHTI QW ARDKFESSFS HKPSLFNKFW QTYSSAEEVL QKIQSGHSLE GCFQVIKLLS RRPRNWSQCV ELARLKFEKY FNHKALQL L HCFPLDIRLK DGSLFWQSPK RPPSPIKFDL NEPLHLSFLQ NAAKLYATVY CIPFAEEDLS ADALLNILSE VKIQEFKPS NKVVQTDETA RKPDHVPISS EDERNAIFQL EKAILSNEAT KSDLQMAVLS FEKDDDHNGH IDFITAASNL RAKMYSIEPA DRFKTKRIA GKIIPAIATT TATVSGLVAL EMIKVTGGYP FEAYKNCFLN LAIPIVVFTE TTEVRKTKIR NGISFTIWDR W TVHGKEDF TLLDFINAVK EKYGIEPTMV VQGVKMLYVP VMPGHAKRLK LTMHKLVKPT TEKKYVDLTV SFAPDIDGDE DL PGPPVRY YFSHDTD

UniProtKB: Ubiquitin-like modifier-activating enzyme 6

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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: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #5: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 5 / 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: 37.84 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: 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: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 188172
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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