5XDA

Structural basis for Ufm1 recognition by UfSP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for Ufm1 recognition by UfSP

Kim, K.H.Ha, B.H.Kim, E.E.

(2018) FEBS Lett 592: 263-273

  • DOI: https://doi.org/10.1002/1873-3468.12951
  • Primary Citation of Related Structures:  
    5XDA

  • PubMed Abstract: 

    Ubiquitin and ubiquitin-like proteins (Ubls) are involved in a variety of cellular functions, and dysfunction of these proteins often leads to disease, thus requiring the precise molecular recognition of the partner. Here, we report a structural basis for the recognition of Ufm1 by the Ufm1-specific protease (UfSP), both from Caenorhabditis elegans. Ufm1 functions in endoplasmic reticulum homeostasis, cell cycle regulation, and dysfunctions of this protein can result in breast cancer and neurological disorders. The structure reveals that in addition to the extended β-structure at the C-terminus of cUfm1, the interactions made by the completely conserved residues in Ufm1 orthologs, Pro88-Val92, corresponding to P6-P2 positions from the cleavage site, seem to be important for the specific recognition of Ufm1 by cUfSP.


  • Organizational Affiliation

    Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ufm1-specific protease
A, B, C, D, E
A, B, C, D, E, F
565Caenorhabditis elegansMutation(s): 1 
Gene Names: odr-8ufsp-2F38A5.1
EC: 3.4.22
UniProt
Find proteins for Q94218 (Caenorhabditis elegans)
Explore Q94218 
Go to UniProtKB:  Q94218
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94218
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-fold modifier 1
G, H, I, J, K
G, H, I, J, K, L
84Caenorhabditis elegansMutation(s): 1 
Gene Names: ufm-1tag-277ZK652.3
UniProt
Find proteins for P34661 (Caenorhabditis elegans)
Explore P34661 
Go to UniProtKB:  P34661
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP34661
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.29 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 267.447α = 90
b = 455.326β = 90
c = 195.558γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
GRLKorea, Republic Of20110021713

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-07
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description