6F09 | pdb_00006f09

Binary complex of 14-3-3 zeta with ubiquitin specific protease 8 (USP8) pSer718 peptide

PDB DOI: https://doi.org/10.2210/pdb6F09/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-11-17 Released: 2018-03-07
Deposition Author(s): Centorrino, F., Ballone, A., Ottmann, C., Guo, S., Leysen, S.
Funding Organization(s): H2020 Marie Curie Actions of the European Commission

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free:
0.225 (Depositor), 0.226 (DCC)
R-Value Work:
0.180 (Depositor), 0.183 (DCC)
R-Value Observed:
0.182 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Biophysical and structural insight into the USP8/14-3-3 interaction.

Centorrino, F., Ballone, A., Wolter, M., Ottmann, C.

(2018) FEBS Lett 592: 1211-1220

PubMed: 29473952 Search on PubMed
DOI: https://doi.org/10.1002/1873-3468.13017
Primary Citation Related Structures:
6F09

PubMed Abstract:
The ubiquitin-specific protease 8 (USP8)/14-3-3 protein-protein interaction has recently been shown to exert a significant role in the pathogenesis of Cushing's disease (CD). USP8 is a deubiquitinase that prevents epidermal growth factor receptor (EGFR) degradation. Impairment of 14-3-3 binding leads to a higher deubiquitination of EGFR and results in a higher EGFR signaling and an increased production of adrenocorticotropic hormone. Here we report the high-resolution crystal structure of the 14-3-3 binding motif of USP8 surrounding Ser718 in complex with 14-3-3ζ and characterize the interaction with fluorescence polarization and isothermal titration calorimetry. Furthermore, we analyze the effect of USP8 mutations identified in CD on binding to 14-3-3.

Organizational Affiliation

Laboratory of Chemical Biology, Department of Biomedical Engineering, Institute for Complex Molecular Systems, Eindhoven University of Technology, The Netherlands.

Macromolecule Content

Total Structure Weight: 111.69 kDa
Atom Count: 7,997
Modeled Residue Count: 941
Deposited Residue Count: 972
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
14-3-3 protein zeta/delta	A [auth P], C [auth Q], E [auth R], G [auth S]	230	Homo sapiens	Mutation(s): 0 Gene Names: YWHAZ
UniProt & NIH Common Fund Data Resources
Find proteins for P63104 (Homo sapiens) Explore P63104 Go to UniProtKB: P63104
PHAROS: P63104 GTEx: ENSG00000164924
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63104
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 8	B [auth A], D [auth B], F [auth C], H [auth D]	13	Homo sapiens	Mutation(s): 0 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for P40818 (Homo sapiens) Explore P40818 Go to UniProtKB: P40818
PHAROS: P40818 GTEx: ENSG00000138592
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40818
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	B [auth A], D [auth B], F [auth C], H [auth D]	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.59 Å
R-Value Free: 0.225 (Depositor), 0.226 (DCC)
R-Value Work: 0.180 (Depositor), 0.183 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.379	α = 99.71
b = 64.89	β = 114.22
c = 71.519	γ = 108.79

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2018-03-07

Deposition Author(s):

Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	Netherlands	Grant Agreement 675179

Revision History (Full details and data files)

Version 1.0: 2018-03-07
Type: Initial release
Version 1.1: 2018-04-25
Changes: Data collection, Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-16
Changes: Structure summary