Crystal structure of Ufm1 in complex with UBA5

Experimental Data Snapshot

  • Resolution: 2.55 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Structural and Functional Analysis of a Novel Interaction Motif within UFM1-activating Enzyme 5 (UBA5) Required for Binding to Ubiquitin-like Proteins and Ufmylation.

Habisov, S.Huber, J.Ichimura, Y.Akutsu, M.Rogova, N.Loehr, F.McEwan, D.G.Johansen, T.Dikic, I.Doetsch, V.Komatsu, M.Rogov, V.V.Kirkin, V.

(2016) J Biol Chem 291: 9025-9041

  • DOI: https://doi.org/10.1074/jbc.M116.715474
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The covalent conjugation of ubiquitin-fold modifier 1 (UFM1) to proteins generates a signal that regulates transcription, response to cell stress, and differentiation. Ufmylation is initiated by ubiquitin-like modifier activating enzyme 5 (UBA5), which activates and transfers UFM1 to ubiquitin-fold modifier-conjugating enzyme 1 (UFC1). The details of the interaction between UFM1 and UBA5 required for UFM1 activation and its downstream transfer are however unclear. In this study, we described and characterized a combined linear LC3-interacting region/UFM1-interacting motif (LIR/UFIM) within the C terminus of UBA5. This single motif ensures that UBA5 binds both UFM1 and light chain 3/γ-aminobutyric acid receptor-associated proteins (LC3/GABARAP), two ubiquitin (Ub)-like proteins. We demonstrated that LIR/UFIM is required for the full biological activity of UBA5 and for the effective transfer of UFM1 onto UFC1 and a downstream protein substrate both in vitro and in cells. Taken together, our study provides important structural and functional insights into the interaction between UBA5 and Ub-like modifiers, improving the understanding of the biology of the ufmylation pathway.

  • Organizational Affiliation

    From Translational Innovation Platform Oncology, Merck KGaA, Frankfurter Strasse 250, 64293 Darmstadt, Germany, the Institute of Biochemistry II, Goethe University School of Medicine, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany, the BMLS Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Riedberg Campus, Max-von-Laue-Strasse 15, 60438 Frankfurt am Main, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-fold modifier 1
A, C
86Homo sapiensMutation(s): 0 
Gene Names: UFM1C13orf20BM-002
UniProt & NIH Common Fund Data Resources
Find proteins for P61960 (Homo sapiens)
Explore P61960 
Go to UniProtKB:  P61960
PHAROS:  P61960
GTEx:  ENSG00000120686 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61960
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ASP-ASN-GLU-TRP-GLY-ILE-GLU-LEU-VAL9Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZZ9 (Homo sapiens)
Explore Q9GZZ9 
Go to UniProtKB:  Q9GZZ9
GTEx:  ENSG00000081307 
Entity Groups  
UniProt GroupQ9GZZ9
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.55 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.198 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.656α = 90
b = 82.656β = 90
c = 62.027γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-09
    Type: Initial release
  • Version 1.1: 2016-10-12
    Changes: Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description