Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B 

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: light scattering

Macromolecule Content

• Total Structure Weight: 55656.43 
• Atom Count: 3679 
• Residue Count: 488 
• Unique protein chains: 2

5OHP

Crystal structure of USP30 (C77A) in complex with Lys6-linked diubiquitin

• DOI: 10.2210/pdb5OHP/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 4 


• Deposited: 2017-07-17 Released: 2017-09-20 
• Deposition Author(s): Gersch, M., Komander, D.
• Funding Organization(s): Medical Research Council (United Kingdom) 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.249 
• R-Value Work: 0.216 

Literature

Mechanism and regulation of the Lys6-selective deubiquitinase USP30.

Gersch, M., Gladkova, C., Schubert, A.F., Michel, M.A., Maslen, S., Komander, D.

(2017) Nat. Struct. Mol. Biol. 24: 920-930

• PubMed: 28945249 
• DOI: 10.1038/nsmb.3475
• Primary Citation of Related Structures:  
  5OHN, 5OHK


• PubMed Abstract: 
  

Damaged mitochondria undergo mitophagy, a specialized form of autophagy that is initiated by the protein kinase PINK1 and the ubiquitin E3 ligase Parkin. Ubiquitin-specific protease USP30 antagonizes Parkin-mediated ubiquitination events on mitochondria and is a key negative regulator of mitophagy. Parkin and USP30 both show a preference for assembly or disassembly, respectively, of Lys6-linked polyubiquitin, a chain type that has not been well studied. Here we report crystal structures of human USP30 bound to monoubiquitin and Lys6-linked diubiquitin, which explain how USP30 achieves Lys6-linkage preference through unique ubiquitin binding interfaces. We assess the interplay between USP30, PINK1 and Parkin and show that distally phosphorylated ubiquitin chains impair USP30 activity. Lys6-linkage-specific affimers identify numerous mitochondrial substrates for this modification, and we show that USP30 regulates Lys6-polyubiquitinated TOM20. Our work provides insights into the architecture, activity and regulation of USP30, which will aid drug design against this and related enzymes.

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Organizational Affiliation: 

Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin carboxyl-terminal hydrolase 30	A	336	Homo sapiens	Mutation(s): 4  Gene Names: USP30 EC: 3.4.19.12
Find proteins for Q70CQ3 (Homo sapiens) Go to Gene View: USP30 Go to UniProtKB:  Q70CQ3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Polyubiquitin-B	B, C	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens) Go to Gene View: UBB Go to UniProtKB:  P0CG47

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.8 Å
• R-Value Free: 0.249 
• R-Value Work: 0.216 
• Space Group: P 6₅ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 117.504	α = 90.00
b = 117.504	β = 90.00
c = 138.842	γ = 120.00

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
Aimless	data scaling
DIALS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-07-17 
• Released Date: 2017-09-20 
• Deposition Author(s): Gersch, M., Komander, D.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	U105192732

Revision History 

• Version 1.0: 2017-09-20
  Type: Initial release
• Version 1.1: 2017-10-04
  Type: Database references
• Version 1.2: 2017-11-15
  Type: Database references
• Version 1.3: 2019-05-08
  Type: Advisory, Data collection, Derived calculations
• Version 1.4: 2019-07-10
  Type: Data collection