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- EMDB-49946: Nucleic acid bound human SLFN14, State 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-49946
TitleNucleic acid bound human SLFN14, State 1
Map data
Sample
  • Complex: Nucleic acid bound SLFN14 complex, state 1
    • Protein or peptide: Protein SLFN14
    • RNA: RNA (5'-R(P*AP*UP*GP*GP*G)-3')
    • RNA: RNA (5'-R(P*CP*CP*CP*AP*CP*UP*C)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
Keywordsnuclease / antiviral factor / post-transcriptional regulator / RNA BINDING PROTEIN
Function / homology
Function and homology information


platelet maturation / rRNA catabolic process / cellular response to magnesium ion / mRNA catabolic process / cellular response to manganese ion / RNA endonuclease activity / ribosome binding / Hydrolases; Acting on ester bonds / ATP binding / nucleus / cytoplasm
Similarity search - Function
: / Schlafen, GTPase-like domain / Schlafen family / Orthopoxvirus B3 protein / Poxviridae B3 protein / Schlafen, AlbA_2 domain / Schlafen, AlbA_2 domain superfamily / Schlafen, AlbA_2 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.73 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_49946.png

Downloads & links

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Map

FileDownload / File: emd_49946.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0519
Minimum - Maximum-0.06236581 - 1.9131067
Average (Standard dev.)0.0016811246 (±0.027390597)
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_49946_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: #2

Fileemd_49946_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Nucleic acid bound SLFN14 complex, state 1

EntireName: Nucleic acid bound SLFN14 complex, state 1
Components
  • Complex: Nucleic acid bound SLFN14 complex, state 1
    • Protein or peptide: Protein SLFN14
    • RNA: RNA (5'-R(P*AP*UP*GP*GP*G)-3')
    • RNA: RNA (5'-R(P*CP*CP*CP*AP*CP*UP*C)-3')
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Nucleic acid bound SLFN14 complex, state 1

SupramoleculeName: Nucleic acid bound SLFN14 complex, state 1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 232 KDa

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Macromolecule #1: Protein SLFN14

MacromoleculeName: Protein SLFN14 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 107.658367 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MESLKTDTEM PYPEVIVDVG RVIFGEENRK KMTNSCLKRS ENSRIIRAIC ALLNSGGGVI KAEIDDKTYS YQCHGLGQDL ETSFQKLLP SGSQKYLDYM QQGHNLLIFV KSWSPDVFSL PLRICSLRSN LYRRDVTSAI NLSASSALEL LREKGFRAQR G RPRVKKLH ...String:
MESLKTDTEM PYPEVIVDVG RVIFGEENRK KMTNSCLKRS ENSRIIRAIC ALLNSGGGVI KAEIDDKTYS YQCHGLGQDL ETSFQKLLP SGSQKYLDYM QQGHNLLIFV KSWSPDVFSL PLRICSLRSN LYRRDVTSAI NLSASSALEL LREKGFRAQR G RPRVKKLH PQQVLNRCIQ EEEDMRILAS EFFKKDKLMY KEKLNFTEST HVEFKRFTTK KVIPRIKEML PHYVSAFANT QG GYVLIGV DDKSKEVVGC KWEKVNPDLL KKEIENCIEK LPTFHFCCEK PKVNFTTKIL NVYQKDVLDG YVCVIQVEPF CCV VFAEAP DSWIMKDNSV TRLTAEQWVV MMLDTQSAPP SLVTDYNSCL ISSASSARKS PGYPIKVHKF KEALQRHLFP VTQE EVQFK PESLCKKLFS DHKELEGLMK TLIHPCSQGI VIFSRSWAGD VGFRKEQNVL CDALLIAVNS PVVLYTILID PNWPG GLEY ARNTAHQLKQ KLQTVGGYTG KVCIIPRLIH LSSTQSRPGE IPLRYPRSYR LADEEEMEDL LQALVVVSLS SRSLLS DQM GCEFFNLLIM EQSQLLSESL QKTRELFIYC FPGVRKTALA IKIMEKIKDL FHCKPKEILY VCESDSLKDF VTQQTTC QA VTRKTFMQGE FLKIKHIVMD ETENFCSKYG NWYMKAKNIT HPKAKGTGSE NLHHGILWLF LDPFQIHHAD VNGLPPPS A QFPRKTITSG IHCALEIAKV MKEEMKRIKE NPPSNMSPDT LALFSETAYE EATCAQALPG VCETKTNLTT EQIANYVAR KCHSLFQCGY LPKDIAILCR RGEDRGRYRL ALLKAMELIE THRPSEVVFS PATGVWGSHI VLDSIQQFSG LERTVVFGLS PECDQSEEF HKLCFASRAI KHLYLLYEKR AAYTRTRPLE QKLISEEDLA ANDILDYKDD DDKV

UniProtKB: Protein SLFN14

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Macromolecule #2: RNA (5'-R(P*AP*UP*GP*GP*G)-3')

MacromoleculeName: RNA (5'-R(P*AP*UP*GP*GP*G)-3') / type: rna / ID: 2 / Details: arbitrary RNA sequence / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.626032 KDa
SequenceString:
AUGGG

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Macromolecule #3: RNA (5'-R(P*CP*CP*CP*AP*CP*UP*C)-3')

MacromoleculeName: RNA (5'-R(P*CP*CP*CP*AP*CP*UP*C)-3') / type: rna / ID: 3 / Details: arbitrary RNA sequence / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 2.116323 KDa
SequenceString:
CCCACUC

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: INSILICO MODEL / Details: Used alphafold model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 338469
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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