6EI1 | pdb_00006ei1

Crystal structure of the covalent complex between deubiquitinase ZUFSP (ZUP1) and Ubiquitin-PA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free: 
    0.203 (Depositor), 0.209 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.173 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6EI1

This is version 1.3 of the entry. See complete history

Literature

A family of unconventional deubiquitinases with modular chain specificity determinants.

Hermanns, T.Pichlo, C.Woiwode, I.Klopffleisch, K.Witting, K.F.Ovaa, H.Baumann, U.Hofmann, K.

(2018) Nat Commun 9: 799-799

  • DOI: https://doi.org/10.1038/s41467-018-03148-5
  • Primary Citation Related Structures: 
    6EI1

  • PubMed Abstract: 

    Deubiquitinating enzymes (DUBs) regulate ubiquitin signaling by trimming ubiquitin chains or removing ubiquitin from modified substrates. Similar activities exist for ubiquitin-related modifiers, although the enzymes involved are usually not related. Here, we report human ZUFSP (also known as ZUP1 and C6orf113) and fission yeast Mug105 as founding members of a DUB family different from the six known DUB classes. The crystal structure of human ZUFSP in covalent complex with propargylated ubiquitin shows that the DUB family shares a fold with UFM1- and Atg8-specific proteases, but uses a different active site more similar to canonical DUB enzymes. ZUFSP family members differ widely in linkage specificity through differential use of modular ubiquitin-binding domains (UBDs). While the minimalistic Mug105 prefers K48 chains, ZUFSP uses multiple UBDs for its K63-specific endo-DUB activity. K63 specificity, localization, and protein interaction network suggest a role for ZUFSP in DNA damage response.


  • Organizational Affiliation
    • Institute for Genetics, University of Cologne, Zülpicher Str. 47a, 50674, Cologne, Germany.

Macromolecule Content 

  • Total Structure Weight: 48.51 kDa 
  • Atom Count: 3,565 
  • Modeled Residue Count: 410 
  • Deposited Residue Count: 422 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger with UFM1-specific peptidase domain protein347Homo sapiensMutation(s): 0 
Gene Names: ZUFSPC6orf113
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q96AP4 (Homo sapiens)
Explore Q96AP4 
Go to UniProtKB:  Q96AP4
PHAROS:  Q96AP4
GTEx:  ENSG00000153975 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96AP4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Polyubiquitin-B75Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
GTEx:  ENSG00000170315 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.73 Å
  • R-Value Free:  0.203 (Depositor), 0.209 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.173 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.23α = 90
b = 84.23β = 90
c = 201.78γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-03-14
    Changes: Structure summary
  • Version 1.2: 2019-10-16
    Changes: Data collection
  • Version 1.3: 2025-04-09
    Changes: Data collection, Database references, Structure summary