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- EMDB-53193: Structure of UBA6-BIRC6 (cluster 4) -

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Basic information

Entry
Database: EMDB / ID: EMD-53193
TitleStructure of UBA6-BIRC6 (cluster 4)
Map data
Sample
  • Complex: UBA6 bound to BIRC6
    • Protein or peptide: Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsE1 / 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 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / regulation of cytokinesis / negative regulation of extrinsic apoptotic signaling pathway / trans-Golgi network / spindle pole / ubiquitin-protein transferase activity / Signaling by ALK fusions and activated point mutants / Antigen processing: Ubiquitination & Proteasome degradation / regulation of cell population proliferation / midbody / ubiquitin-dependent protein catabolic process / cell population proliferation / protein phosphorylation / endosome / protein ubiquitination / cell division / positive regulation of cell population proliferation / apoptotic process / DNA damage response / centrosome / negative regulation of apoptotic process / ATP binding / metal ion binding / nucleus / membrane / cytoplasm / cytosol
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
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme 6 / Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.15 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 17, 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_53193.png

Downloads & links

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Map

FileDownload / File: emd_53193.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å		0.83 Å/pix.
x 320 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.825 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.22878745 - 0.6183476
Average (Standard dev.)-0.0009459701 (±0.027364096)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 264.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53193_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53193_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_53193_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 : UBA6 bound to BIRC6

EntireName: UBA6 bound to BIRC6
Components
  • Complex: UBA6 bound to BIRC6
    • Protein or peptide: Dual E2 ubiquitin-conjugating enzyme/E3 ubiquitin-protein ligase BIRC6
    • Protein or peptide: Ubiquitin-like modifier-activating enzyme 6
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: UBA6 bound to BIRC6

SupramoleculeName: UBA6 bound to BIRC6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 150 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: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*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: 37.45 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: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 9889
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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