4A3P

Structure of USP15 DUSP-UBL deletion mutant

PDB DOI: https://doi.org/10.2210/pdb4A3P/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: 1.40 Å
R-Value Free: 0.221
R-Value Work: 0.153
R-Value Observed: 0.157

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

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 Search on PubMed
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. P.R.Elliott@liv.ac.uk

Macromolecule Content

Total Structure Weight: 25.33 kDa
Atom Count: 1,965
Modelled Residue Count: 210
Deposited Residue Count: 217
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN CARBOXYL-TERMINAL HYDROLASE 15	A	217	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y4E8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.221
R-Value Work: 0.153
R-Value Observed: 0.157
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.95	α = 90
b = 44.25	β = 104.33
c = 56.15	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-11-16

Deposition Author(s):

Revision History (Full details and data files)

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