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- EMDB-49947: Nucleic acid bound human SLFN14, State 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-49947
TitleNucleic acid bound human SLFN14, State 2
Map data
Sample
  • Complex: nucleic-acid bound SLFN14 protein
Keywordsnuclease / antiviral factor / post-transcriptional regulator / RNA BINDING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsVan Riper J / Martinez-Claros AO / Wang L / Schneiderman H / Maheshwari S / Pillon MC
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)R00ES030735 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM147123 United States
Cancer Prevention and Research Institute of Texas (CPRIT)RR200076 United States
CitationJournal: Nat Commun / Year: 2025
Title: CryoEM structure of the SLFN14 endoribonuclease reveals insight into RNA binding and cleavage.
Authors: Justin Van Riper / Arleth O Martinez-Claros / Lie Wang / Hannah E Schneiderman / Sweta Maheshwari / Monica C Pillon /
Abstract: The SLFN14 endoribonuclease is a post-transcriptional regulator that targets the ribosome and its associated RNA substrates for codon-bias translational repression. SLFN14 nuclease activity is linked ...The SLFN14 endoribonuclease is a post-transcriptional regulator that targets the ribosome and its associated RNA substrates for codon-bias translational repression. SLFN14 nuclease activity is linked to antiviral defense and platelet function. Despite its prominent role in gene regulation, the molecular signals regulating SLFN14 substrate recognition and catalytic activation remain unclear. SLFN14 dysregulation is linked to human diseases, including ribosomopathies and inherited thrombocytopenia, thus underscoring the importance of establishing the signals coordinating its RNA processing activity. Here, we reconstitute active full-length human SLFN14 and report a high-resolution cryoEM reconstruction of the SLFN14•RNA complex. The structure reveals a medallion-like architecture that shares structural homology with other SLFN family members. We unveil a C-terminal hydrophobic intermolecular interface that stabilizes the SLFN14 homodimer without the need for additional molecular signals. We describe compact sequence-independent RNA binding interfaces and highlight the environment of the SLFN14 disease hotspot at the RNA cleft entrance. We show that the SLFN14 endoribonuclease has broad site-specificity in the absence of modified native tRNA, a characteristic not shared with its SLFN11 family member. Finally, we demonstrate that metal-dependent acceptor stem cleavage requires the SLFN14 E-EhK motif and uncover its unexpected parallel with other virus-activatable nucleases.
History
DepositionMar 29, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49947.png

Downloads & links

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Map

FileDownload / File: emd_49947.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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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å		0.83 Å/pix.
x 300 pix.
= 249.6 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0519
Minimum - Maximum-0.034998633 - 2.241794
Average (Standard dev.)0.0019429034 (±0.030582912)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 249.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_49947_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_49947_half_map_2.map
Projections & Slices
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Sample components

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Entire : nucleic-acid bound SLFN14 protein

EntireName: nucleic-acid bound SLFN14 protein
Components
  • Complex: nucleic-acid bound SLFN14 protein

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Supramolecule #1: nucleic-acid bound SLFN14 protein

SupramoleculeName: nucleic-acid bound SLFN14 protein / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 50.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / 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: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 188010
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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