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- EMDB-64191: Electronic microscopy structure of human schlafen14-E211A dimer i... -
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Open data
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Basic information
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Title | Electronic microscopy structure of human schlafen14-E211A dimer in complex with dsRNA | |||||||||
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![]() | Dimer / RNase / complex / RNA BINDING PROTEIN/RNA / RNA BINDING PROTEIN-RNA complex | |||||||||
Function / homology | ![]() 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 | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.88 Å | |||||||||
![]() | Mengyun L / Dapeng S / Wei H / Yumei W / Sheng C | |||||||||
Funding support | 1 items
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![]() | ![]() 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 |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 60 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.1 KB 17.1 KB | Display Display | ![]() |
Images | ![]() | 63.7 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() | 49.7 MB 49.7 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1023.5 KB | Display | ![]() |
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Full document | ![]() | 1023.1 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 14.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9uieMC ![]() 9jr9C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.78813 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_64191_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_64191_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex of human schlafen 14 E211A dimer with dsRNA
Entire | Name: Complex of human schlafen 14 E211A dimer with dsRNA |
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Components |
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-Supramolecule #1: Complex of human schlafen 14 E211A dimer with dsRNA
Supramolecule | Name: Complex of human schlafen 14 E211A dimer with dsRNA / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: RNA (32-MER)
Macromolecule | Name: RNA (32-MER) / type: rna / ID: 1 / Number of copies: 1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 10.265141 KDa |
Sequence | String: GCAUCAGCUA CCUAAAGUUC AGGUAGCUGA UG |
-Macromolecule #2: Protein SLFN14
Macromolecule | Name: Protein SLFN14 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 103.945234 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 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 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 289 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 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 stage | Specimen 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
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Output model | ![]() PDB-9uie: |