8Q1S | pdb_00008q1s

Pathogenic mutations of human phosphorylation sites affect protein-protein interactions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free: 
    0.279 (Depositor), 0.279 (DCC) 
  • R-Value Work: 
    0.230 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 
    0.233 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8Q1S

This is version 1.2 of the entry. See complete history

Literature

Pathogenic mutations of human phosphorylation sites affect protein-protein interactions.

Rrustemi, T.Meyer, K.Roske, Y.Uyar, B.Akalin, A.Imami, K.Ishihama, Y.Daumke, O.Selbach, M.

(2024) Nat Commun 15: 3146-3146

  • DOI: https://doi.org/10.1038/s41467-024-46794-8
  • Primary Citation Related Structures: 
    8Q1S

  • PubMed Abstract: 

    Despite their lack of a defined 3D structure, intrinsically disordered regions (IDRs) of proteins play important biological roles. Many IDRs contain short linear motifs (SLiMs) that mediate protein-protein interactions (PPIs), which can be regulated by post-translational modifications like phosphorylation. 20% of pathogenic missense mutations are found in IDRs, and understanding how such mutations affect PPIs is essential for unraveling disease mechanisms. Here, we employ peptide-based interaction proteomics to investigate 36 disease-associated mutations affecting phosphorylation sites. Our results unveil significant differences in interactomes between phosphorylated and non-phosphorylated peptides, often due to disrupted phosphorylation-dependent SLiMs. We focused on a mutation of a serine phosphorylation site in the transcription factor GATAD1, which causes dilated cardiomyopathy. We find that this phosphorylation site mediates interaction with 14-3-3 family proteins. Follow-up experiments reveal the structural basis of this interaction and suggest that 14-3-3 binding affects GATAD1 nucleocytoplasmic transport by masking a nuclear localisation signal. Our results demonstrate that pathogenic mutations of human phosphorylation sites can significantly impact protein-protein interactions, offering insights into potential molecular mechanisms underlying pathogenesis.


  • Organizational Affiliation
    • Max Delbrück Center (MDC), Robert-Rössle-Str. 10, 13125, Berlin, Germany.

Macromolecule Content 

  • Total Structure Weight: 62.22 kDa 
  • Atom Count: 3,935 
  • Modeled Residue Count: 489 
  • Deposited Residue Count: 540 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
14-3-3 protein epsilon
A, B
255Homo sapiensMutation(s): 0 
Gene Names: YWHAE
UniProt & NIH Common Fund Data Resources
Find proteins for P62258 (Homo sapiens)
Explore P62258 
Go to UniProtKB:  P62258
PHAROS:  P62258
GTEx:  ENSG00000108953 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62258
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GATA zinc finger domain-containing protein 1C,
D [auth P]
15Homo sapiensMutation(s): 0 
Gene Names: GATAD1ODAG
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUU5 (Homo sapiens)
Explore Q8WUU5 
Go to UniProtKB:  Q8WUU5
PHAROS:  Q8WUU5
GTEx:  ENSG00000157259 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WUU5
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.23 Å
  • R-Value Free:  0.279 (Depositor), 0.279 (DCC) 
  • R-Value Work:  0.230 (Depositor), 0.234 (DCC) 
  • R-Value Observed: 0.233 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 123.78α = 90
b = 123.78β = 90
c = 250.2γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-04-24
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Structure summary