8VIV | pdb_00008viv

Crystal structure of FBF-2 RBD in complex with gld-1 FBEa* RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.232 (Depositor), 0.232 (DCC) 
  • R-Value Work: 
    0.197 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.199 (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

A higher order PUF complex is central to regulation of C. elegans germline stem cells.

Qiu, C.Crittenden, S.L.Carrick, B.H.Dillard, L.B.Costa Dos Santos, S.J.Dandey, V.P.Dutcher, R.C.Viverette, E.G.Wine, R.N.Woodworth, J.Campbell, Z.T.Wickens, M.Borgnia, M.J.Kimble, J.Hall, T.M.T.

(2025) Nat Commun 16: 123-123

  • DOI: https://doi.org/10.1038/s41467-024-55526-x
  • Primary Citation of Related Structures:  
    8VIV

  • PubMed Abstract: 

    PUF RNA-binding proteins are broadly conserved stem cell regulators. Nematode PUF proteins maintain germline stem cells (GSCs) and, with key partner proteins, repress differentiation mRNAs, including gld-1. Here we report that PUF protein FBF-2 and its partner LST-1 form a ternary complex that represses gld-1 via a pair of adjacent FBF binding elements (FBEs) in its 3'UTR. One LST-1 molecule links two FBF-2 molecules via motifs in the LST-1 intrinsically-disordered region; the gld-1 FBE pair includes a well-established 'canonical' FBE and a newly-identified noncanonical FBE. Remarkably, this FBE pair drives both full RNA repression in GSCs and full RNA activation upon differentiation. Discoveries of the LST-1-FBF-2 ternary complex, the gld-1 adjacent FBEs, and their in vivo significance predict an expanded regulatory repertoire of different assemblies of PUF-partner-RNA higher order complexes in nematode GSCs. This also suggests analogous PUF controls may await discovery in other biological contexts and organisms.


  • Organizational Affiliation
    • Epigenetics and RNA Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.

Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fem-3 mRNA-binding factor 2413Caenorhabditis elegansMutation(s): 0 
Gene Names: fbf-2F21H12.5
UniProt
Find proteins for Q09312 (Caenorhabditis elegans)
Explore Q09312 
Go to UniProtKB:  Q09312
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09312
Sequence Annotations
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  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(*CP*AP*UP*GP*UP*UP*GP*CP*CP*AP*U)-3')11Caenorhabditis elegans
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.232 (Depositor), 0.232 (DCC) 
  • R-Value Work:  0.197 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.199 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.569α = 90
b = 98.569β = 90
c = 107.14γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SERGUIdata collection
Cootmodel building
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references