9NYY | pdb_00009nyy

Nucleic acid bound human SLFN14, State 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

CryoEM structure of the SLFN14 endoribonuclease reveals insight into RNA binding and cleavage.

Van Riper, J.Martinez-Claros, A.O.Wang, L.Schneiderman, H.E.Maheshwari, S.Pillon, M.C.

(2025) Nat Commun 16: 5848-5848

  • DOI: https://doi.org/10.1038/s41467-025-61091-8
  • Primary Citation of Related Structures:  
    9NYY

  • PubMed 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 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.


  • Organizational Affiliation
    • Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX, USA.

Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein SLFN14
A, B
943Homo sapiensMutation(s): 0 
Gene Names: SLFN14
EC: 3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P0C7P3 (Homo sapiens)
Explore P0C7P3 
Go to UniProtKB:  P0C7P3
PHAROS:  P0C7P3
GTEx:  ENSG00000236320 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C7P3
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
RNA (5'-R(P*AP*UP*GP*GP*G)-3')5Homo sapiens
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
RNA (5'-R(P*CP*CP*CP*AP*CP*UP*C)-3')7Homo sapiens
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.73 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1_5286

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 StatesR00ES030735
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM147123
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRR200076

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Data collection, Database references