5GVI

Zebrafish USP30 in complex with Lys6-linked diubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural basis for specific cleavage of Lys6-linked polyubiquitin chains by USP30

Sato, Y.Okatsu, K.Saeki, Y.Yamano, K.Matsuda, N.Kaiho, A.Yamagata, A.Goto-Ito, S.Ishikawa, M.Hashimoto, Y.Tanaka, K.Fukai, S.

(2017) Nat. Struct. Mol. Biol. 24: 911-919

  • DOI: 10.1038/nsmb.3469

  • PubMed Abstract: 
  • Parkin ubiquitin (Ub) ligase (also known as PARK2) ubiquitinates damaged mitochondria for their clearance and quality control. USP30 deubiquitinase opposes parkin-mediated Ub-chain formation on mitochondria by preferentially cleaving Lys6-linked Ub c ...

    Parkin ubiquitin (Ub) ligase (also known as PARK2) ubiquitinates damaged mitochondria for their clearance and quality control. USP30 deubiquitinase opposes parkin-mediated Ub-chain formation on mitochondria by preferentially cleaving Lys6-linked Ub chains. Here, we report the crystal structure of zebrafish USP30 in complex with a Lys6-linked diubiquitin (diUb or Ub2) at 1.87-Å resolution. The distal Ub-recognition mechanism of USP30 is similar to those of other USP family members, whereas Phe4 and Thr12 of the proximal Ub are recognized by a USP30-specific surface. Structure-based mutagenesis showed that the interface with the proximal Ub is critical for the specific cleavage of Lys6-linked Ub chains, together with the noncanonical catalytic triad composed of Cys-His-Ser. The structural findings presented here reveal a mechanism for Lys6-linkage-specific deubiquitination.


    Organizational Affiliation

    Structural Life Science Division, Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 30
A
444N/AMutation(s): 2 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ubiquitin
B
76Mus musculusMutation(s): 1 
Gene Names: Rps27a (Uba80, Ubcep1)
Find proteins for P62983 (Mus musculus)
Go to UniProtKB:  P62983
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
ubiquitin
C
72Mus musculusMutation(s): 0 
Gene Names: Rps27a (Uba80, Ubcep1)
Find proteins for P62983 (Mus musculus)
Go to UniProtKB:  P62983
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.176 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 130.270α = 90.00
b = 130.270β = 90.00
c = 59.881γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-09-05 
  • Released Date: 2017-09-13 
  • Deposition Author(s): Sato, Y., Fukai, S.

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan16H04750
Japan Society for the Promotion of ScienceJapan24687012
Japan Society for the Promotion of ScienceJapan15H01175
Japan Society for the Promotion of ScienceJapan25112505
Japan Society for the Promotion of ScienceJapan25117711
Japan Society for the Promotion of ScienceJapan22121003
Japan Society for the Promotion of ScienceJapan24247014
Japan Science and Technology AgencyJapan--

Revision History 

  • Version 1.0: 2017-09-13
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Data collection, Database references
  • Version 1.2: 2017-10-18
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Database references