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- PDB-9nyy: Nucleic acid bound human SLFN14, State 1 -

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Basic information

Entry
Database: PDB / ID: 9nyy
TitleNucleic acid bound human SLFN14, State 1
Components
  • Protein SLFN14
  • RNA (5'-R(P*AP*UP*GP*GP*G)-3')
  • RNA (5'-R(P*CP*CP*CP*AP*CP*UP*C)-3')
KeywordsRNA BINDING PROTEIN / nuclease / antiviral factor / post-transcriptional regulator
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
RNA / Protein SLFN14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.73 Å
AuthorsVan Riper, J. / Martinez-Claros, A.O. / Wang, L. / Schneiderman, H. / Maheshwari, S. / Pillon, M.C.
Funding support United States, 3items
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, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release
Revision 1.1Jul 16, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein SLFN14
B: Protein SLFN14
C: RNA (5'-R(P*AP*UP*GP*GP*G)-3')
D: RNA (5'-R(P*CP*CP*CP*AP*CP*UP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,2639
Polymers219,0594
Non-polymers2045
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein SLFN14


Mass: 107658.367 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLFN14 / Production host: Homo sapiens (human)
References: UniProt: P0C7P3, Hydrolases; Acting on ester bonds
#2: RNA chain RNA (5'-R(P*AP*UP*GP*GP*G)-3')


Mass: 1626.032 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: arbitrary RNA sequence / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: RNA chain RNA (5'-R(P*CP*CP*CP*AP*CP*UP*C)-3')


Mass: 2116.323 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: arbitrary RNA sequence / Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Nucleic acid bound SLFN14 complex, state 1 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Molecular weightValue: 0.232 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50.2 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.73 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 338469 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 47.12 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002813742
ELECTRON MICROSCOPYf_angle_d0.56918584
ELECTRON MICROSCOPYf_chiral_restr0.04082102
ELECTRON MICROSCOPYf_plane_restr0.00482299
ELECTRON MICROSCOPYf_dihedral_angle_d8.53791937

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