9F6G | pdb_00009f6g

Human USP30 chimera bound to Ubiquitin-PA

• PDB DOI: https://doi.org/10.2210/pdb9F6G/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-05-01 Released: 2025-03-19 
• Deposition Author(s): Kazi, N.H., Gersch, M.
• Funding Organization(s): Max Planck Society

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Models: in silico, experimental

Literature

Chimeric deubiquitinase engineering reveals structural basis for specific inhibition of the mitophagy regulator USP30

Kazi, N.H., Klink, N., Gallant, K., Kipka, G.M., Gersch, M.

(2025) Nat Struct Mol Biol 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: cross-linking

Macromolecule Content

• Total Structure Weight: 44.7 kDa 
• Atom Count: 3,126 
• Modelled Residue Count: 356 
• Deposited Residue Count: 392 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 30,Ubiquitin carboxyl-terminal hydrolase 14,Ubiquitin carboxyl-terminal hydrolase 35	A	317	Homo sapiens	Mutation(s): 1  Gene Names: USP30, USP14, TGT, USP35, KIAA1372, USP34 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for P54578 (Homo sapiens) Explore P54578  Go to UniProtKB:  P54578
PHAROS:  P54578 GTEx:  ENSG00000101557
Find proteins for Q9P2H5 (Homo sapiens) Explore Q9P2H5  Go to UniProtKB:  Q9P2H5
PHAROS:  Q9P2H5 GTEx:  ENSG00000118369
Find proteins for Q70CQ3 (Homo sapiens) Explore Q70CQ3  Go to UniProtKB:  Q70CQ3
PHAROS:  Q70CQ3 GTEx:  ENSG00000135093
UniProt Groups	P54578Q70CQ3Q9P2H5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	B	75	Homo sapiens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AYE (Subject of Investigation/LOI)	C [auth A]	prop-2-en-1-amine C3 H7 N VVJKKWFAADXIJK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.211 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.639	α = 90
b = 50.706	β = 90
c = 156.56	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
xia2	data reduction
Aimless	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Kazi, N.H., Gersch, M.

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Funding Organization	Location	Grant Number
Max Planck Society	Germany	CGCIII-352S

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release