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- EMDB-45096: The FBF-2/LST-1/gld-1 RNA complex (one FBF-2) -

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Basic information

Entry
Database: EMDB / ID: EMD-45096
TitleThe FBF-2/LST-1/gld-1 RNA complex (one FBF-2)
Map data
Sample
  • Complex: Ternary complex of FBF-2 with LST-1 and RNA
    • Protein or peptide: FBF-2
    • Protein or peptide: LST-1
    • RNA: gld-1 RNA
KeywordsPumillio RNA-binding protein / RNA BINDING PROTEIN
Biological speciesCaenorhabditis elegans (invertebrata) / Caenorhabditis elegans/Monacrosporium haptotylum mixed EST library (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsQiu C / Hall TMT
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS) United States
CitationJournal: Nat Commun / Year: 2025
Title: A higher order PUF complex is central to regulation of C. elegans germline stem cells.
Authors: Chen Qiu / Sarah L Crittenden / Brian H Carrick / Lucas B Dillard / Stephany J Costa Dos Santos / Venkata P Dandey / Robert C Dutcher / Elizabeth G Viverette / Robert N Wine / Jennifer ...Authors: Chen Qiu / Sarah L Crittenden / Brian H Carrick / Lucas B Dillard / Stephany J Costa Dos Santos / Venkata P Dandey / Robert C Dutcher / Elizabeth G Viverette / Robert N Wine / Jennifer Woodworth / Zachary T Campbell / Marvin Wickens / Mario J Borgnia / Judith Kimble / Traci M Tanaka Hall /
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 ...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.
History
DepositionMay 28, 2024-
Header (metadata) releaseDec 25, 2024-
Map releaseDec 25, 2024-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45096.png

Downloads & links

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Map

FileDownload / File: emd_45096.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å		0.93 Å/pix.
x 300 pix.
= 279.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.2590383 - 1.9044749
Average (Standard dev.)-0.00005993427 (±0.03579487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 279.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_45096_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_45096_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of FBF-2 with LST-1 and RNA

EntireName: Ternary complex of FBF-2 with LST-1 and RNA
Components
  • Complex: Ternary complex of FBF-2 with LST-1 and RNA
    • Protein or peptide: FBF-2
    • Protein or peptide: LST-1
    • RNA: gld-1 RNA

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Supramolecule #1: Ternary complex of FBF-2 with LST-1 and RNA

SupramoleculeName: Ternary complex of FBF-2 with LST-1 and RNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Caenorhabditis elegans (invertebrata)

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Macromolecule #1: FBF-2

MacromoleculeName: FBF-2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans/Monacrosporium haptotylum mixed EST library (eukaryote)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSNNVLPTWS LDSNGEMRSR LSLSEVLDSG DLMKFAVDKT GCQFLEKAVK GSLTSYQKFQ LFEQVIGRKD DFLKLSTNIF GNYLVQSVIG ISLATNDDGY TKRQEKLKNF ISSQMTDMCL DKFACRVIQS SLQNMDLSLA CKLVQALPRD ARLIAICVDQ NANHVIQKVV ...String:
GSNNVLPTWS LDSNGEMRSR LSLSEVLDSG DLMKFAVDKT GCQFLEKAVK GSLTSYQKFQ LFEQVIGRKD DFLKLSTNIF GNYLVQSVIG ISLATNDDGY TKRQEKLKNF ISSQMTDMCL DKFACRVIQS SLQNMDLSLA CKLVQALPRD ARLIAICVDQ NANHVIQKVV AVIPLKNWEF IVDFVATPEH LRQICSDKYG CRVVQTIIEK LTADSMNVDL TSAAQNLRER ALQRLMTSVT NRCQELATNE YANYIIQHIV SNDDLAVYRE CIIEKCLMRN LLSLSQEKFA SHVVEKAFLH APLELLAEMM DEIFDGYIPH PDTGKDALDI MMFHQFGNYV VQCMLTICCD AVSGRRQTKE GGYDHAISFQ DWLKKLHSRV TKERHRLSRF SSGKKMIETL ANLRSTHPIY ELQ

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Macromolecule #2: LST-1

MacromoleculeName: LST-1 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSNSTIAYSK SQHEAPKQLL QLRSEIKPLI PLNQPSNFWE SSQDSGVLSS LSSSPQQRSG LRSQKLHLTY IEKNKRVRAM IPQ

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Macromolecule #3: gld-1 RNA

MacromoleculeName: gld-1 RNA / type: rna / ID: 3
Source (natural)Organism: Caenorhabditis elegans (invertebrata)
SequenceString:
AUCAUGUGCC AUACAUCAUG UUGCCAUUU

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7.4 / Details: 20 mM HEPES pH 7.4, 150 mM NaCl, and 2 mM DTT
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 252126
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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