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 
  • R-Value Observed: 0.178 

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: https://doi.org/10.1038/nsmb.3469
  • Primary Citation of Related Structures:  
    5GVI

  • 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 chains ...

    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 Ub 2 ) 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: 

    CREST, Japan Science and Technology Agency, Tokyo, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 30A444Danio rerioMutation(s): 2 
Gene Names: usp30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ubiquitinB76Mus musculusMutation(s): 1 
Gene Names: Rps27a, Uba80, Ubcep1
UniProt
Find proteins for P62983 (Mus musculus)
Explore P62983 
Go to UniProtKB:  P62983
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62983
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
ubiquitinC72Mus musculusMutation(s): 0 
Gene Names: Rps27a, Uba80, Ubcep1
UniProt
Find proteins for P62983 (Mus musculus)
Explore P62983 
Go to UniProtKB:  P62983
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62983
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
D [auth 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 
  • R-Value Observed: 0.178 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.27α = 90
b = 130.27β = 90
c = 59.881γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

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  (Full details and data files)

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