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- PDB-9jn9: Cryo-EM structure of human SLFN14 -

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Basic information

Entry
Database: PDB / ID: 9jn9
TitleCryo-EM structure of human SLFN14
ComponentsProtein SLFN14
KeywordsHYDROLASE / DNA/RNA processing enzymes
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsLuo, M. / Jia, X.D. / Wang, Z.W. / Yang, J.Y. / Zhang, Q.F. / Gao, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82173098 China
CitationJournal: Nucleic Acids Res / Year: 2025
Title: Structural and functional characterization of human SLFN14.
Authors: Meng Luo / Xudong Jia / Zi-Wen Wang / Jin-Yu Yang / Wen Wang / Jiazhen Chen / Jun-Ying Ou / Jian-Xiong Feng / Bing Yu / Sheng Wang / Lin Huang / Neil V Morgan / Kai Deng / Tongsheng Chen / ...Authors: Meng Luo / Xudong Jia / Zi-Wen Wang / Jin-Yu Yang / Wen Wang / Jiazhen Chen / Jun-Ying Ou / Jian-Xiong Feng / Bing Yu / Sheng Wang / Lin Huang / Neil V Morgan / Kai Deng / Tongsheng Chen / Qinfen Zhang / Song Gao /
Abstract: The Schlafen (SLFN) family of proteins are a group of DNA/RNA processing enzymes with emerging importance in human health and disease, where their functions are implicated in a variety of ...The Schlafen (SLFN) family of proteins are a group of DNA/RNA processing enzymes with emerging importance in human health and disease, where their functions are implicated in a variety of immunological and anti-tumor processes. Here, we present the cryo-electron microscopy structure of full-length human SLFN14, a member with antiviral activity and linked to an inherited bleeding disorder. SLFN14 is composed of an RNase domain, a SWADL domain, and a two-lobe helicase domain. SLFN14 exhibited strong RNase activity over different substrates, and the positively charged patches at the valley of the RNase domain, which contains the thrombocytopenia-related missense mutation sites, are crucial for binding oligonucleotides. SLFN14 lacks helicase activity, which can be attributed to the inability to bind ATP and the absence of positive charges at the canonical DNA-binding site of its RecA-like folds. SLFN14 is structurally similar to SLFN11, but differs from SLFN5 in the orientation of the helicase domain. Live-cell fluorescence resonance energy transfer (FRET) assays and AlphaFold2 analysis hinted that SLFN14 may adopt multiple conformations in cells. These results provide detailed structural and biochemical features of SLFN14, and greatly expand our knowledge of the functional diversity of the SLFN family.
History
DepositionSep 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 18, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein SLFN14
B: Protein SLFN14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,7834
Polymers209,6532
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Protein SLFN14


Mass: 104826.312 Da / Num. of mol.: 2 / Mutation: E206A/E211A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLFN14 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P0C7P3, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / 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: SLFN14 dimer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 209.36 kDa/nm / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7 / Details: 20mM HEPES,300mM NaCl,1mM DTT
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid mesh size: 300 divisions/in.
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: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 735934 / Symmetry type: POINT

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