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- EMDB-61794: Cryo-EM structure of bovine UBA7-UBE2L6-ISG15 -

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Basic information

Entry
Database: EMDB / ID: EMD-61794
TitleCryo-EM structure of bovine UBA7-UBE2L6-ISG15
Map data
Sample
  • Complex: Complex structure of bovine UBA7-UBE2L6-ISG15
    • Protein or peptide: UBA7 protein
    • Protein or peptide: Ubiquitin/ISG15-conjugating enzyme E2 L6
    • Protein or peptide: Ubiquitin-like protein ISG15
  • Ligand: ADENOSINE MONOPHOSPHATE
Keywordscryo-EM / UBA7 / UBE2L6 / ISG15 / IMMUNE SYSTEM
Function / homology
Function and homology information


ISG15 antiviral mechanism / Modulation of host responses by IFN-stimulated genes / ubiquitin-like modifier activating enzyme activity / ISG15 transferase activity / PKR-mediated signaling / ISG15-protein conjugation / positive regulation of protein oligomerization / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / regulation of type II interferon production ...ISG15 antiviral mechanism / Modulation of host responses by IFN-stimulated genes / ubiquitin-like modifier activating enzyme activity / ISG15 transferase activity / PKR-mediated signaling / ISG15-protein conjugation / positive regulation of protein oligomerization / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / regulation of type II interferon production / protein localization to mitochondrion / response to type I interferon / negative regulation of type I interferon-mediated signaling pathway / E2 ubiquitin-conjugating enzyme / negative regulation of viral genome replication / ubiquitin conjugating enzyme activity / positive regulation of interleukin-10 production / positive regulation of bone mineralization / negative regulation of protein ubiquitination / positive regulation of interferon-beta production / positive regulation of erythrocyte differentiation / integrin-mediated signaling pathway / modification-dependent protein catabolic process / positive regulation of type II interferon production / protein tag activity / protein polyubiquitination / integrin binding / ubiquitin-dependent protein catabolic process / defense response to virus / protein ubiquitination / defense response to bacterium / ubiquitin protein ligase binding / extracellular region / ATP binding / nucleus / cytoplasm
Similarity search - Function
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 / 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 / : / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / 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 / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Ubiquitin/ISG15-conjugating enzyme E2 L6 / Ubiquitin-like protein ISG15 / UBA7 protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsChen P-T / Wu K-P
Funding support Taiwan, 1 items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Elife / Year: 2025
Title: Elucidating the Mechanism Underlying UBA7-UBE2L6 Disulfide Complex Formation.
Authors: Chen P-T / Yeh J-Y / Weng J-H / Wu K-P
History
DepositionOct 3, 2024-
Header (metadata) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 19, 2025-
Current statusMar 19, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61794.png

Downloads & links

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Map

FileDownload / File: emd_61794.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 432 pix.
= 279.936 Å		0.65 Å/pix.
x 432 pix.
= 279.936 Å		0.65 Å/pix.
x 432 pix.
= 279.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.648 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.038054273 - 2.1620636
Average (Standard dev.)0.0007185255 (±0.017024446)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions432432432
Spacing432432432
CellA=B=C: 279.936 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_61794_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61794_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex structure of bovine UBA7-UBE2L6-ISG15

EntireName: Complex structure of bovine UBA7-UBE2L6-ISG15
Components
  • Complex: Complex structure of bovine UBA7-UBE2L6-ISG15
    • Protein or peptide: UBA7 protein
    • Protein or peptide: Ubiquitin/ISG15-conjugating enzyme E2 L6
    • Protein or peptide: Ubiquitin-like protein ISG15
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: Complex structure of bovine UBA7-UBE2L6-ISG15

SupramoleculeName: Complex structure of bovine UBA7-UBE2L6-ISG15 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Bos taurus (domestic cattle)

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Macromolecule #1: UBA7 protein

MacromoleculeName: UBA7 protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 110.119859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDTLETSKLL DKELYSRQLY VLGLPAMQRI QGAKVLLSGL QGLGAEVAKN LVLMGVGSLT LHDPHPTCWS DLAAQFLLSE QDLGRSRAE ASQKLLAELN GAVQVSVYTG DITKDLLLDF QVVVLTASRL EEQLRVGTLC HEHGVCFLVA DTRGLVGQLF C DFGENFTV ...String:
MDTLETSKLL DKELYSRQLY VLGLPAMQRI QGAKVLLSGL QGLGAEVAKN LVLMGVGSLT LHDPHPTCWS DLAAQFLLSE QDLGRSRAE ASQKLLAELN GAVQVSVYTG DITKDLLLDF QVVVLTASRL EEQLRVGTLC HEHGVCFLVA DTRGLVGQLF C DFGENFTV QDPTEAEPLT ANIQHISQGS PGILTLREEA GTHHFHTGDW VTFSGIEGMV ELNGCDPRPL HVREDGTLEI GD TTAFSCY LRGGAVTEVK RAKTVSHEPL DTALLQPRVV AQSAQKVRAR CLHQSFRALH KFQQLHGRPP KPWDPVDAEM VVD LAQAMG PLKGTEGEPL EEQLDEALVR TVALSSAGGL SPMAAVLGAV AAQEVLKAIS GKFMPLDQWL YFDALDCLPE DGDP FPNPE DCAPRRCRYD GQTAVFGTNF QEKLSHQHYL LVGAGAVGCE LLKSFALMGL GAGDGGGVTV ADMDHVELSN LSRQF LFRS QDIHRKKAEV AAEATRRLNA DLQVTPLNLQ LDPTTEDIFG DDFFSGVNGV AAALDTFEAR DYVAARCTHF LKPLLE AGT MGTRGSASVF IPHVTENYKA PSDAASEDAP DPVCTVRYIP ATTEHTVQWA KGEFDDLFCE SAKTINSHPQ ALSSPED LV KSQKQPLLQT MRGVLTERPQ TWQDCVLWAF GHWQLRFHYG ITQLLRTYPP DKVQEDGTPF WSGPKQCPQP LKFDASQD M HLLYVLAAAN LYAQMHGLPG SQDQTALRGL LNLLPLPDPQ NLDRIFASEL ELDSPSGCKQ LHEDLKTWSK GPPLKPLTF EKDNDSNFHV DFVVAAASLR AQNYGIPVAS HAETKRIVGR IIPAVVTTTA AVAGLVGLEL YKVVGGPRPR HAFRHSYLHL AENYFSRWV PKAPDIQKFH HLKWTCWDRL EVPAGQPERT LESLLAHIQE LQGLRVTMLL HGSALLYSAG WSEEKQTQHL S RRVTDLVK KVPGQRVLVL ELGYEGEEDD TNFPRLHYKL

UniProtKB: UBA7 protein

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Macromolecule #2: Ubiquitin/ISG15-conjugating enzyme E2 L6

MacromoleculeName: Ubiquitin/ISG15-conjugating enzyme E2 L6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: E2 ubiquitin-conjugating enzyme
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 18.597215 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAASKRVAKE LEDLQKELPK YLRNLSSEED NVLVWHALLL PERPPYNLKA FRLSISFPRE YPFQPPTVKF TTRIYHPNVD RDGRVCLPI ISKKNWKAST RTSQVLEALN MLVNQPEPGQ PVRLELAEQL TQDPELFDQM AQEFTLQFGV DRPSHHHHHH

UniProtKB: Ubiquitin/ISG15-conjugating enzyme E2 L6

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Macromolecule #3: Ubiquitin-like protein ISG15

MacromoleculeName: Ubiquitin-like protein ISG15 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (domestic cattle)
Molecular weightTheoretical: 17.330094 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGGDLTVKML GGQEILVPLR DSMTVSELKQ FIAQKINVPA FQQRLAHLDS REVLQEGVPL VLQGLRAGST VLLVVQNCIS ILVRNDKGR SSPYEVQLKQ TVAELKQQVC QKERVQADQF WLSFEGRPMD DEHPLEEYGL MKGCTVFMNL RLRGG

UniProtKB: Ubiquitin-like protein ISG15

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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: 7.6
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: AlphaFold
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 176617
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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