9CI7 | pdb_00009ci7

Structure of PNUTS:Tox4 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.217 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

PNUTS:PP1 recruitment to Tox4 regulates chromosomal dispersal in Drosophila germline development.

Duncalf, L.Wang, X.Aljabri, A.A.Campbell, A.E.Alharbi, R.Q.Donaldson, I.Hayes, A.Peti, W.Page, R.Bennett, D.

(2025) Cell Rep 44: 115693-115693

  • DOI: https://doi.org/10.1016/j.celrep.2025.115693
  • Primary Citation of Related Structures:  
    9CI7

  • PubMed Abstract: 

    Ser/Thr protein phosphatase 1 (PP1) forms a large nuclear holoenzyme (with PNUTS, WDR82, and Tox4) whose emerging role is to regulate transcription. However, the role of Tox4, and its interplay with the other phosphatase subunits in this complex, is poorly understood. Here, we combine biochemical, structural, cellular, and in vivo experiments to show that, while tox4 is dispensable for viability, it is essential for fertility, having both PNUTS-dependent and -independent roles in Drosophila germline development. We also show that Tox4 requires zinc for PNUTS TFIIS N-terminal domain (TND) binding, and that it binds the TND on a surface distinct from that used by established TND-interacting transcriptional regulators. We also show that selective disruption of the PNUTS-Tox4 and the PNUTS-PP1 interaction is critical for normal gene expression and chromosomal dispersal during oogenesis. Together, these data demonstrate how interactions within the PNUTS-Tox4-PP1 phosphatase combine to tune transcriptional outputs driving developmental transitions.


  • Organizational Affiliation
    • Faculty of Health and Life Sciences, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB Liverpool, UK.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 1 regulatory subunit 10159Rattus norvegicusMutation(s): 1 
Gene Names: Ppp1r10Cat53Pnuts
UniProt
Find proteins for O55000 (Rattus norvegicus)
Explore O55000 
Go to UniProtKB:  O55000
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO55000
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TOX high mobility group box family member 454Homo sapiensMutation(s): 1 
Gene Names: TOX4C14orf92KIAA0737
UniProt & NIH Common Fund Data Resources
Find proteins for O94842 (Homo sapiens)
Explore O94842 
Go to UniProtKB:  O94842
PHAROS:  O94842
GTEx:  ENSG00000092203 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO94842
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
I [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.217 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.63α = 90
b = 70.63β = 90
c = 97.165γ = 120
Software Package:
Software NamePurpose
RESOLVEmodel building
PHENIXrefinement
XDSdata reduction
SOLVEphasing
Cootmodel building
Aimlessdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States144379
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States144483

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release