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- EMDB-64191: Electronic microscopy structure of human schlafen14-E211A dimer i... -

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Basic information

Entry
Database: EMDB / ID: EMD-64191
TitleElectronic microscopy structure of human schlafen14-E211A dimer in complex with dsRNA
Map data
Sample
  • Organelle or cellular component: Complex of human schlafen 14 E211A dimer with dsRNA
    • RNA: RNA (32-MER)
    • Protein or peptide: Protein SLFN14
  • Ligand: ZINC ION
KeywordsDimer / RNase / complex / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex
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: 2.88 Å
AuthorsMengyun L / Dapeng S / Wei H / Yumei W / Sheng C
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Adv Sci (Weinh) / Year: 2025
Title: Human Schlafen 14 Cleavage of Short Double-Stranded RNAs Underpins its Antiviral Activity.
Authors: Mengyun Li / Dapeng Sun / Wei Hao / Hua Fu / Yueli Zhang / Zhijian Li / Bo Qin / Yumei Wang / Sheng Cui /
Abstract: The Schlafen (SLFN) genes are induced by interferons, underscoring their roles in the immune response and viral replication inhibition. SLFN14, a member of SLFN family, is associated with multiple ...The Schlafen (SLFN) genes are induced by interferons, underscoring their roles in the immune response and viral replication inhibition. SLFN14, a member of SLFN family, is associated with multiple human diseases; however, neither its functions nor its disease mechanisms are fully understood. Herein, human SLFN14 biochemically is characterized, demonstrating that it specifically cleaves RNAs containing short duplex regions, such as hairpin RNAs and tRNAs, but does not have ATPase or helicase activity. Cryogenic electron microscopy structures of SLFN14 apoenzyme (2.84 Å) and SLFN14-hairpin RNA complex (2.88 Å) are determined, revealing that SLFN14 assembles into a ring-like dimer and dimerization is mainly mediated by hydrophobic contacts. Two N-terminal RNase domains of SLFN14 are organized head-to-tail, forming an RNA-binding groove that can accommodate a 12-bp hairpin RNA. The hairpin RNA is recognized mainly through phosphate backbone interactions. Further, SLFN14 is shown to inhibits HIV-1 pseudovirus replication. The anti-HIV-1 activity of SLFN14 is via codon-usage-dependent translational inhibition and impairment of the programmed -1 ribosomal frameshifting, with an efficiency comparable to that of Shiftless. Using tRNA PCR arrays, SLFN14 and SLFN11 are found to decrease both nuclear-encoded and mitochondrial tRNAs in cells. Together, these results provide novel insights into the function of SLFN14 and its role in HIV-1 restriction.
History
DepositionApr 15, 2025-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

Downloads & links

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Map

FileDownload / File: emd_64191.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.79 Å/pix.
x 256 pix.
= 201.76 Å
0.79 Å/pix.
x 256 pix.
= 201.76 Å
0.79 Å/pix.
x 256 pix.
= 201.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.78813 Å
Density
Contour LevelBy AUTHOR: 0.016
Minimum - Maximum-0.08278656 - 0.14677148
Average (Standard dev.)0.00013403887 (±0.0061520273)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 201.76 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_64191_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_64191_half_map_2.map
Projections & Slices
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Sample components

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Entire : Complex of human schlafen 14 E211A dimer with dsRNA

EntireName: Complex of human schlafen 14 E211A dimer with dsRNA
Components
  • Organelle or cellular component: Complex of human schlafen 14 E211A dimer with dsRNA
    • RNA: RNA (32-MER)
    • Protein or peptide: Protein SLFN14
  • Ligand: ZINC ION

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Supramolecule #1: Complex of human schlafen 14 E211A dimer with dsRNA

SupramoleculeName: Complex of human schlafen 14 E211A dimer with dsRNA / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: RNA (32-MER)

MacromoleculeName: RNA (32-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.265141 KDa
SequenceString:
GCAUCAGCUA CCUAAAGUUC AGGUAGCUGA UG

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Macromolecule #2: Protein SLFN14

MacromoleculeName: Protein SLFN14 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 103.945234 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 HVAFKRFTTK KVIPRIKEML PHYVSAFANT QG GYVLIGV DDKSKEVVGC KWEKVNPDLL KKEIENCIEK LPTFHFCCEK PKVNFTTKIL NVYQKDVLDG YVCVIQVEPF CCV VFAEAP DSWIMKDNSV TRLTAEQWVV MMLDTQSAPP SLVTDYNSSL 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 EATSAQALPG VCETKTNLTT EQIANYVAR KCHSLFQSGY LPKDIAILCR RGEDRGRYRL ALLKAMELIE THRPSEVVFS PATGVWGSHI VLDSIQQFSG LERTVVFGLS PECDQSEEF HKLCFASRAI KHLYLLYEKR AAY

UniProtKB: Protein SLFN14

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 7.5 / Component - Concentration: 150.0 mm/L / Component - Formula: NaCl / Component - Name: sodium chloride / Details: 10 mM Tris-HCL, 150 mM NaCl, 2 mM MgCl2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 338615
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-9uie:
Electronic microscopy structure of human schlafen14-E211A dimer in complex with dsRNA

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