4A3O

Crystal structure of the USP15 DUSP-UBL monomer

• PDB DOI: https://doi.org/10.2210/pdb4A3O/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2011-10-03 Released: 2011-11-16 
• Deposition Author(s): Elliott, P.R., Liu, H., Pastok, M.W., Grossmann, G.J., Rigden, D.J., Clague, M.J., Urbe, S., Barsukov, I.L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.229 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 

Starting Model: experimental

Literature

Structural Variability of the Ubiquitin Specific Protease Dusp-Ubl Double Domains.

Elliott, P.R., Liu, H., Pastok, M.W., Grossmann, G.J., Rigden, D.J., Clague, M.J., Urbe, S., Barsukov, I.L.

(2011) FEBS Lett 585: 3385

• PubMed: 22001210 
• DOI: https://doi.org/10.1016/j.febslet.2011.09.040
• Primary Citation of Related Structures:  
  3PV1, 4A3O, 4A3P


• PubMed Abstract: 
  

  USP4, 11 and 15 are three closely related paralogues of the ubiquitin specific protease (USP) family of deubiquitinating enzymes. The DUSP domain and the UBL domain in these proteins are juxtaposed which may provide a functional unit conferring specificity. We determined the structures of the USP15 DUSP-UBL double domain unit in monomeric and dimeric states. We then conducted comparative analysis of the structural and physical properties of all three DUSP-UBL units. We identified structural features that dictate different dispositions between constituent domains, which in turn may influence respective binding properties.

---

Organizational Affiliation: 

The University of Liverpool, Institute of Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7ZB, United Kingdom. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 51.21 kDa 
• Atom Count: 3,719 
• Modelled Residue Count: 423 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15	A, B	220	Homo sapiens	Mutation(s): 0  EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y4E8 (Homo sapiens) Explore Q9Y4E8  Go to UniProtKB:  Q9Y4E8
PHAROS:  Q9Y4E8 GTEx:  ENSG00000135655

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.229 
• R-Value Work: 0.201 
• R-Value Observed: 0.202 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.419	α = 90
b = 100.419	β = 90
c = 71.704	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-16 
Deposition Author(s): Elliott, P.R., Liu, H., Pastok, M.W., Grossmann, G.J., Rigden, D.J., Clague, M.J., Urbe, S., Barsukov, I.L.

Revision History  

• Version 1.0: 2011-11-16
  Type: Initial release
  
• Version 1.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description