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- PDB-9jtc: Cryo-EM structure of bovine UBA7-UBE2L6-ISG15 -

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Basic information

Entry
Database: PDB / ID: 9jtc
TitleCryo-EM structure of bovine UBA7-UBE2L6-ISG15
Components
  • UBA7 protein
  • Ubiquitin-like protein ISG15
  • Ubiquitin/ISG15-conjugating enzyme E2 L6
KeywordsIMMUNE SYSTEM / cryo-EM / UBA7 / UBE2L6 / ISG15
Function / homology
Function and homology information


ISG15 antiviral mechanism / Modulation of host responses by IFN-stimulated genes / ISG15 transferase activity / ubiquitin-like modifier activating enzyme activity / PKR-mediated signaling / ISG15-protein conjugation / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / positive regulation of protein oligomerization / regulation of type II interferon production ...ISG15 antiviral mechanism / Modulation of host responses by IFN-stimulated genes / ISG15 transferase activity / ubiquitin-like modifier activating enzyme activity / PKR-mediated signaling / ISG15-protein conjugation / Termination of translesion DNA synthesis / Negative regulators of DDX58/IFIH1 signaling / positive regulation of protein oligomerization / 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 / integrin binding / protein tag activity / positive regulation of type II interferon production / protein polyubiquitination / ubiquitin-dependent protein catabolic process / defense response to virus / defense response to bacterium / protein ubiquitination / 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 / 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
ADENOSINE MONOPHOSPHATE / Ubiquitin/ISG15-conjugating enzyme E2 L6 / Ubiquitin-like protein ISG15 / UBA7 protein
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.99 Å
AuthorsChen, P.-T. / Wu, K.-P.
Funding support Taiwan, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 5, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UBA7 protein
B: Ubiquitin/ISG15-conjugating enzyme E2 L6
C: Ubiquitin-like protein ISG15
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,3944
Polymers146,0473
Non-polymers3471
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein UBA7 protein / Ubiquitin E1-like enzyme


Mass: 110119.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: UBA7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5GF34
#2: Protein Ubiquitin/ISG15-conjugating enzyme E2 L6 / E2 ubiquitin-conjugating enzyme L6 / Ubiquitin carrier protein L6 / Ubiquitin-protein ligase L6


Mass: 18597.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: UBE2L6 / Production host: Escherichia coli (E. coli)
References: UniProt: A5PJC4, E2 ubiquitin-conjugating enzyme
#3: Protein Ubiquitin-like protein ISG15 / Interferon-stimulated gene product 17 / Ubiquitin cross-reactive protein / BoUCRP


Mass: 17330.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: ISG15, G1P2, ISG17, UCRP / Production host: Escherichia coli (E. coli) / References: UniProt: O02741
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex structure of bovine UBA7-UBE2L6-ISG15 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Bos taurus (domestic cattle)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.99 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 176617 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0039374
ELECTRON MICROSCOPYf_angle_d0.52812735
ELECTRON MICROSCOPYf_dihedral_angle_d13.043471
ELECTRON MICROSCOPYf_chiral_restr0.0391415
ELECTRON MICROSCOPYf_plane_restr0.0041665

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