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- EMDB-61620: Cryo-EM structure of human SLFN14 -

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Basic information

Entry
Database: EMDB / ID: EMD-61620
TitleCryo-EM structure of human SLFN14
Map data
Sample
  • Complex: SLFN14 dimer
    • Protein or peptide: Protein SLFN14
  • Ligand: ZINC ION
KeywordsDNA/RNA processing enzymes / HYDROLASE
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: 3.36 Å
AuthorsLuo M / Jia XD / Wang ZW / Yang JY / Zhang QF / Gao S
Funding support China, 1 items
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, 2024-
Header (metadata) releaseJun 18, 2025-
Map releaseJun 18, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61620.png

Downloads & links

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Map

FileDownload / File: emd_61620.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 218.88 Å		0.86 Å/pix.
x 256 pix.
= 218.88 Å		0.86 Å/pix.
x 256 pix.
= 218.88 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-0.8711572 - 54.873860000000001
Average (Standard dev.)0.000000000060653 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 218.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_61620_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #2

Fileemd_61620_half_map_2.map
Projections & Slices
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Sample components

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Entire : SLFN14 dimer

EntireName: SLFN14 dimer
Components
  • Complex: SLFN14 dimer
    • Protein or peptide: Protein SLFN14
  • Ligand: ZINC ION

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Supramolecule #1: SLFN14 dimer

SupramoleculeName: SLFN14 dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 209.36 kDa/nm

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Macromolecule #1: Protein SLFN14

MacromoleculeName: Protein SLFN14 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.826312 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: GPHMGGSEFM ESLKTDTEMP YPEVIVDVGR VIFGEENRKK MTNSCLKRSE NSRIIRAICA LLNSGGGVIK AEIDDKTYSY QCHGLGQDL ETSFQKLLPS GSQKYLDYMQ QGHNLLIFVK SWSPDVFSLP LRICSLRSNL YRRDVTSAIN LSASSALELL R EKGFRAQR ...String:
GPHMGGSEFM ESLKTDTEMP YPEVIVDVGR VIFGEENRKK MTNSCLKRSE NSRIIRAICA LLNSGGGVIK AEIDDKTYSY QCHGLGQDL ETSFQKLLPS GSQKYLDYMQ QGHNLLIFVK SWSPDVFSLP LRICSLRSNL YRRDVTSAIN LSASSALELL R EKGFRAQR GRPRVKKLHP QQVLNRCIQE EEDMRILASE FFKKDKLMYK EKLNFTASTH VAFKRFTTKK VIPRIKEMLP HY VSAFANT QGGYVLIGVD DKSKEVVGCK WEKVNPDLLK KEIENCIEKL PTFHFCCEKP KVNFTTKILN VYQKDVLDGY VCV IQVEPF CCVVFAEAPD SWIMKDNSVT RLTAEQWVVM MLDTQSAPSS LVTDYNSCLI SSASSARKSP GYPIKVHKFK EALQ RHLFP VTQEEVQFKP ESLCKKLFSD HKELEGLMKT LIHPCSQGIV IFSRSWAGDV GFRKEQNVLC DALLIAVNSP VVLYT ILID PNWPGGLEYA RNTAHQLKQK LQTVGGYTGK VCIIPRLIHL SSTQSRPGEI PLRYPRSYRL ADEEEMEDLL QALVVV SLS SRSLLSDQMG CEFFNLLIME QSQLLSESLQ KTRELFIYCF PGVRKTALAI KIMEKIKDLF HCKPKEILYV CESDSLK DF VTQQTTCQAV TRKTFMQGEF LKIKHIVMDE TENFCSKYGN WYMKAKNITH PKAKGTGSEN LHHGILWLFL DPFQIHHA D VNGLPPPSAQ FPRKTITSGI HCALEIAKVM KEEMKRIKEN PPSNMSPDTL ALFSETAYEE ATCAQALPGV CETKTNLTT EQIANYVARK CHSLFQCGYL PKDIAILCRR GEDRGRYRLA LLKAMELIET HRPSEVVFSP ATGVWGSHIV LDSIQQFSGL ERTVVFGLS PECDQSEEFH KLCFASRAIK HLYLLYEKRA AY

UniProtKB: Protein SLFN14

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / 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

Concentration0.5 mg/mL
BufferpH: 7 / Details: 20mM HEPES,300mM NaCl,1mM DTT
GridMesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 735934
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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