7LRQ

Crystal structure of human SFPQ/NONO heterodimer, conserved DBHS region


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 

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

Paraspeckle subnuclear bodies depend on dynamic heterodimerisation of DBHS RNA-binding proteins via their structured domains.

Lee, P.W.Marshall, A.C.Knott, G.J.Kobelke, S.Martelotto, L.Cho, E.McMillan, P.J.Lee, M.Bond, C.S.Fox, A.H.

(2022) J Biol Chem 298: 102563-102563

  • DOI: https://doi.org/10.1016/j.jbc.2022.102563
  • Primary Citation of Related Structures:  
    7LRQ

  • PubMed Abstract: 

    RNA-binding proteins of the DBHS (Drosophila Behavior Human Splicing) family, NONO, SFPQ, and PSPC1 have numerous roles in genome stability and transcriptional and posttranscriptional regulation. Critical to DBHS activity is their recruitment to distinct subnuclear locations, for example, paraspeckle condensates, where DBHS proteins bind to the long noncoding RNA NEAT1 in the first essential step in paraspeckle formation. To carry out their diverse roles, DBHS proteins form homodimers and heterodimers, but how this dimerization influences DBHS localization and function is unknown. Here, we present an inducible GFP-NONO stable cell line and use it for live-cell 3D-structured illumination microscopy, revealing paraspeckles with dynamic, twisted elongated structures. Using siRNA knockdowns, we show these labeled paraspeckles consist of GFP-NONO/endogenous SFPQ dimers and that GFP-NONO localization to paraspeckles depends on endogenous SFPQ. Using purified proteins, we confirm that partner swapping between NONO and SFPQ occurs readily in vitro. Crystallographic analysis of the NONO-SFPQ heterodimer reveals conformational differences to the other DBHS dimer structures, which may contribute to partner preference, RNA specificity, and subnuclear localization. Thus overall, our study suggests heterodimer partner availability is crucial for NONO subnuclear distribution and helps explain the complexity of both DBHS protein and paraspeckle dynamics through imaging and structural approaches.


  • Organizational Affiliation

    The School of Human Sciences, The University of Western Australia, Crawley, WA, Australia; The Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, and The Centre for Medical Research, The University of Western Australia, Crawley, WA, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor, proline- and glutamine-rich260Homo sapiensMutation(s): 0 
Gene Names: SFPQPSF
UniProt & NIH Common Fund Data Resources
Find proteins for P23246 (Homo sapiens)
Explore P23246 
Go to UniProtKB:  P23246
PHAROS:  P23246
GTEx:  ENSG00000116560 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23246
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Non-POU domain-containing octamer-binding protein260Homo sapiensMutation(s): 0 
Gene Names: NONONRB54
UniProt & NIH Common Fund Data Resources
Find proteins for Q15233 (Homo sapiens)
Explore Q15233 
Go to UniProtKB:  Q15233
PHAROS:  Q15233
GTEx:  ENSG00000147140 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15233
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.258 
  • R-Value Observed: 0.260 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.128α = 90
b = 66.128β = 90
c = 203.561γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia1147496
Australian Research Council (ARC)Australia--

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2022-10-26
    Changes: Database references
  • Version 1.2: 2022-11-23
    Changes: Database references
  • Version 1.3: 2023-10-25
    Changes: Data collection, Refinement description