8OIF

Structure of the UBE1L activating enzyme bound to ISG15 and UBE2L6


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Insights into the ISG15 transfer cascade by the UBE1L activating enzyme.

Wallace, I.Baek, K.Prabu, J.R.Vollrath, R.von Gronau, S.Schulman, B.A.Swatek, K.N.

(2023) Nat Commun 14: 7970-7970

  • DOI: https://doi.org/10.1038/s41467-023-43711-3
  • Primary Citation of Related Structures:  
    8OIF

  • PubMed Abstract: 

    The attachment of the ubiquitin-like protein ISG15 to substrates by specific E1-E2-E3 enzymes is a well-established signalling mechanism of the innate immune response. Here, we present a 3.45 Å cryo-EM structure of a chemically trapped UBE1L-UBE2L6 complex bound to activated ISG15. This structure reveals the details of the first steps of ISG15 recognition and UBE2L6 recruitment by UBE1L (also known as UBA7). Taking advantage of viral effector proteins from severe acute respiratory coronavirus 2 (SARS-CoV-2) and influenza B virus (IBV), we validate the structure and confirm the importance of the ISG15 C-terminal ubiquitin-like domain in the adenylation reaction. Moreover, biochemical characterization of the UBE1L-ISG15 and UBE1L-UBE2L6 interactions enables the design of ISG15 and UBE2L6 mutants with altered selectively for the ISG15 and ubiquitin conjugation pathways. Together, our study helps to define the molecular basis of these interactions and the specificity determinants that ensure the fidelity of ISG15 signalling during the antiviral response.


  • Organizational Affiliation

    Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like modifier-activating enzyme 71,014Homo sapiensMutation(s): 0 
Gene Names: UBA7UBE1LUBE2
UniProt & NIH Common Fund Data Resources
Find proteins for P41226 (Homo sapiens)
Explore P41226 
Go to UniProtKB:  P41226
PHAROS:  P41226
GTEx:  ENSG00000182179 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP41226
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-like protein ISG15B [auth I]157Homo sapiensMutation(s): 0 
Gene Names: ISG15G1P2UCRP
UniProt & NIH Common Fund Data Resources
Find proteins for P05161 (Homo sapiens)
Explore P05161 
Go to UniProtKB:  P05161
PHAROS:  P05161
GTEx:  ENSG00000187608 
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UniProt GroupP05161
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin/ISG15-conjugating enzyme E2 L6C [auth L]155Homo sapiensMutation(s): 0 
Gene Names: UBE2L6UBCH8
EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for O14933 (Homo sapiens)
Explore O14933 
Go to UniProtKB:  O14933
PHAROS:  O14933
GTEx:  ENSG00000156587 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14933
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AMP (Subject of Investigation/LOI)
Query on AMP

Download Ideal Coordinates CCD File 
D [auth I]ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMC_UU_00018/10
Royal SocietyUnited KingdomRGS_R2_222185
Max Planck SocietyGermany--
European Research Council (ERC)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release