9GSU | pdb_00009gsu

Structure of PP1-Neurabin bound to 4E-BP1.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.281 (Depositor), 0.281 (DCC) 
  • R-Value Work: 
    0.242 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 
    0.244 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

PDZ-directed substrate recruitment is the primary determinant of specific 4E-BP1 dephosphorylation by PP1-Neurabin.

Fedoryshchak, R.O.El-Bouri, K.Joshi, D.Mouilleron, S.Treisman, R.

(2025) Elife 13

  • DOI: https://doi.org/10.7554/eLife.103403
  • Primary Citation of Related Structures:  
    9GSU

  • PubMed Abstract: 

    Phosphoprotein phosphatase 1 (PP1) relies on association with PP1-interacting proteins (PIPs) to generate substrate-specific PIP/PP1 holoenzymes, but the lack of well-defined substrates has hindered elucidation of the mechanisms involved. We previously demonstrated that the Phactr1 PIP confers sequence specificity on the Phactr1/PP1 holoenzyme by remodelling the PP1 hydrophobic substrate groove. Phactr1 defines a group of 'RVxF-ΦΦ-R-W' PIPs that all interact with PP1 in a similar fashion. Here, we use a PP1-PIP fusion approach to address sequence specificity and identify substrates of the RVxF-ΦΦ-R-W family PIPs. We show that the four Phactr proteins confer identical sequence specificities on their holoenzymes. We identify the 4E-BP and p70 S6K translational regulators as substrates for the Neurabin/Spinophilin PIPs, implicated in neuronal plasticity, pointing to a role for their holoenzymes in mTORC1-dependent translational control. Biochemical and structural experiments show that in contrast to the Phactrs, substrate recruitment and catalytic efficiency of the PP1-Neurabin and PP1-Spinophilin fusions is primarily determined by substrate interaction with the PDZ domain adjoining their RVxF-ΦΦ-R-W motifs, rather than by recognition of the remodelled PP1 hydrophobic groove. Thus, even PIPs that interact with PP1 in a similar manner use different mechanisms to ensure substrate selectivity.


  • Organizational Affiliation
    • Signalling and Transcription Laboratory, Francis Crick Institute, London, United Kingdom.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphataseA,
C [auth D]
340Homo sapiensMutation(s): 0 
EC: 3.1.3.16
UniProt
Find proteins for A0A7J7RZV7 (Pipistrellus kuhlii)
Explore A0A7J7RZV7 
Go to UniProtKB:  A0A7J7RZV7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7J7RZV7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Neurabin-1B [auth C],
D [auth E]
176Homo sapiensMutation(s): 0 
Gene Names: PPP1R9AKIAA1222
UniProt & NIH Common Fund Data Resources
Find proteins for Q9ULJ8 (Homo sapiens)
Explore Q9ULJ8 
Go to UniProtKB:  Q9ULJ8
PHAROS:  Q9ULJ8
GTEx:  ENSG00000158528 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ULJ8
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.281 (Depositor), 0.281 (DCC) 
  • R-Value Work:  0.242 (Depositor), 0.240 (DCC) 
  • R-Value Observed: 0.244 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.955α = 90
b = 130.647β = 90
c = 156.132γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Francis Crick InstituteUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-18
    Type: Initial release
  • Version 1.1: 2026-01-14
    Changes: Database references