6ZC9 | pdb_00006zc9

Structure of 14-3-3 gamma in complex with Nedd4-2 14-3-3 binding motif Ser448

PDB DOI: https://doi.org/10.2210/pdb6ZC9/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2020-06-10 Released: 2021-07-21
Deposition Author(s): Pohl, P., Kalabova, D., Obsil, T., Obsilova, V.
Funding Organization(s): Czech Science Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.239 (Depositor), 0.241 (DCC)
R-Value Work:
0.212 (Depositor), 0.214 (DCC)
R-Value Observed:
0.213 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

14-3-3-protein regulates Nedd4-2 by modulating interactions between HECT and WW domains.

Pohl, P., Joshi, R., Petrvalska, O., Obsil, T., Obsilova, V.

(2021) Commun Biol 4: 899-899

PubMed: 34294877 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s42003-021-02419-0
Primary Citation Related Structures:
6ZBT, 6ZC9, 7NMZ

PubMed Abstract:
Neural precursor cell expressed developmentally down-regulated 4 ligase (Nedd4-2) is an E3 ubiquitin ligase that targets proteins for ubiquitination and endocytosis, thereby regulating numerous ion channels, membrane receptors and tumor suppressors. Nedd4-2 activity is regulated by autoinhibition, calcium binding, oxidative stress, substrate binding, phosphorylation and 14-3-3 protein binding. However, the structural basis of 14-3-3-mediated Nedd4-2 regulation remains poorly understood. Here, we combined several techniques of integrative structural biology to characterize Nedd4-2 and its complex with 14-3-3. We demonstrate that phosphorylated Ser ³⁴² and Ser ⁴⁴⁸ are the key residues that facilitate 14-3-3 protein binding to Nedd4-2 and that 14-3-3 protein binding induces a structural rearrangement of Nedd4-2 by inhibiting interactions between its structured domains. Overall, our findings provide the structural glimpse into the 14-3-3-mediated Nedd4-2 regulation and highlight the potential of the Nedd4-2:14-3-3 complex as a pharmacological target for Nedd4-2-associated diseases such as hypertension, epilepsy, kidney disease and cancer.

Organizational Affiliation

Department of Structural Biology of Signaling Proteins, Division BIOCEV, Institute of Physiology of the Czech Academy of Sciences, Vestec, Czech Republic.

Macromolecule Content

Total Structure Weight: 113.19 kDa
Atom Count: 7,979
Modeled Residue Count: 941
Deposited Residue Count: 976
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 gamma	A, B, C, D	234	Homo sapiens	Mutation(s): 0 Gene Names: YWHAG
UniProt & NIH Common Fund Data Resources
Find proteins for P61981 (Homo sapiens) Explore P61981 Go to UniProtKB: P61981
PHAROS: P61981 GTEx: ENSG00000170027
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61981
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase NEDD4-like	E, F, G, H	10	Homo sapiens	Mutation(s): 0 EC: 2.3.2.26 (PDB Primary Data), 2.3.2.36 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96PU5 (Homo sapiens) Explore Q96PU5 Go to UniProtKB: Q96PU5
PHAROS: Q96PU5 GTEx: ENSG00000049759
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96PU5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CFH Query on CFH Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth D] SDF format, chain L [auth D] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth D] MOL2 format, chain L [auth D] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth D] mmCIF format, chain L [auth D]	I [auth B], J [auth B], K [auth D], L [auth D]	1,1,1,3,3,3-hexafluoropropan-2-ol C₃ H₂ F₆ O BYEAHWXPCBROCE-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth D] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth D] Focus chain L [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	E, F, G, H	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.239 (Depositor), 0.241 (DCC)
R-Value Work: 0.212 (Depositor), 0.214 (DCC)
R-Value Observed: 0.213 (Depositor)

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 205.707	α = 90
b = 205.707	β = 90
c = 74.649	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-07-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Czech Science Foundation	Czech Republic	20-00058S

Revision History (Full details and data files)

Version 1.0: 2021-07-21
Type: Initial release
Version 1.1: 2021-08-04
Changes: Database references
Version 1.2: 2024-01-24
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-10-23
Changes: Structure summary