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- EMDB-52968: Cryo-EM structure of the helicase core of ZNFX1 -

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Basic information

Entry
Database: EMDB / ID: EMD-52968
TitleCryo-EM structure of the helicase core of ZNFX1
Map data
Sample
  • Complex: ZNFX1
    • Protein or peptide: NFX1-type zinc finger-containing protein 1
  • Ligand: ZINC ION
KeywordsHelicase / E3 ligase / interferon-stimulated gene / RNA BINDING PROTEIN
Function / homology
Function and homology information


nuclear RNA-directed RNA polymerase complex / regulatory ncRNA-mediated heterochromatin formation / negative regulation of viral genome replication / activation of innate immune response / helicase activity / cytoplasmic stress granule / defense response to virus / mitochondrial outer membrane / defense response to bacterium / innate immune response ...nuclear RNA-directed RNA polymerase complex / regulatory ncRNA-mediated heterochromatin formation / negative regulation of viral genome replication / activation of innate immune response / helicase activity / cytoplasmic stress granule / defense response to virus / mitochondrial outer membrane / defense response to bacterium / innate immune response / RNA binding / zinc ion binding
Similarity search - Function
ZNFX1 domain / Zinc finger, NF-X1-type / ZnF_NFX / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7-like helicase / : ...ZNFX1 domain / Zinc finger, NF-X1-type / ZnF_NFX / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / DNA2/NAM7 helicase, helicase domain / AAA domain / DNA2/NAM7-like helicase / : / DNA2/NAM7 helicase-like, C-terminal / AAA domain / Armadillo-type fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
NFX1-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsGrabarczyk DB / Reznikow V / Kurzbauer R / Clausen T
Funding support Austria, European Union, 2 items
OrganizationGrant numberCountry
Austrian Research Promotion Agency Austria
H2020 Marie Curie Actions of the European CommissionEuropean Union
CitationJournal: Cell / Year: 2025
Title: A split-site E3 ligase mechanism enables ZNFX1 to ubiquitinate and cluster single-stranded RNA into ubiquitin-coated nucleoprotein particles.
Authors: Daniel B Grabarczyk / Eric J Aird / Vanessa Reznikow / Paul C Kirchgatterer / Julian F Ehrmann / Robert Kurzbauer / Lillie E Bell / Max J Kellner / Ritika Aggarwal / Alexander Schleiffer / ...Authors: Daniel B Grabarczyk / Eric J Aird / Vanessa Reznikow / Paul C Kirchgatterer / Julian F Ehrmann / Robert Kurzbauer / Lillie E Bell / Max J Kellner / Ritika Aggarwal / Alexander Schleiffer / Victoria Faas / Luiza Deszcz / Anton Meinhart / Gijs A Versteeg / Josef M Penninger / Lukas S Stelzl / Moritz M Gaidt / Ingrid Tessmer / Jacob E Corn / Tim Clausen /
Abstract: Eukaryotic cells use a multi-layered immune response to combat intracellular pathogens. The ubiquitin ligase ZNFX1 has emerged as a crucial yet little understood player that regulates the immune ...Eukaryotic cells use a multi-layered immune response to combat intracellular pathogens. The ubiquitin ligase ZNFX1 has emerged as a crucial yet little understood player that regulates the immune response while protecting against RNA viruses. Our study unveils the molecular mechanism of ZNFX1, mediated by the joint activity of a helicase serving as a nucleic acid sensor and a non-conventional E3 module featuring a split active site. We demonstrate that single-stranded RNA stimulates E3 activity by fostering dimerization of ZNFX1 subunits that translocate along nucleic acid tracks. Juxtaposed E3 domains complement each other, leading to the ubiquitination of ZNFX1 itself and engaged RNA molecules, while clustering nucleic acids into dense nucleoprotein particles. We show that the E3 ligase activity of ZNFX1 protects cells during an immune response and propose that ubiquitin-coated particles formed by ZNFX1 represent part of an ancient mechanism to regulate both foreign and host RNA in the cell.
History
DepositionFeb 27, 2025-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
SupersessionSep 17, 2025ID: EMD-19626
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52968.png

Downloads & links

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Map

FileDownload / File: emd_52968.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 256 pix.
= 304.64 Å		1.19 Å/pix.
x 256 pix.
= 304.64 Å		1.19 Å/pix.
x 256 pix.
= 304.64 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.70172566 - 0.9098984
Average (Standard dev.)0.00063408335 (±0.01879209)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 304.64 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_52968_msk_1.map
Projections & Slices
AxesZYX

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Additional map: Global refinement including ARM and 1Z domains

Fileemd_52968_additional_1.map
AnnotationGlobal refinement including ARM and 1Z domains
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AxesZYX

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Half map: #2

Fileemd_52968_half_map_1.map
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Half map: #1

Fileemd_52968_half_map_2.map
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Sample components

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Entire : ZNFX1

EntireName: ZNFX1
Components
  • Complex: ZNFX1
    • Protein or peptide: NFX1-type zinc finger-containing protein 1
  • Ligand: ZINC ION

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Supramolecule #1: ZNFX1

SupramoleculeName: ZNFX1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: NFX1-type zinc finger-containing protein 1

MacromoleculeName: NFX1-type zinc finger-containing protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 166.098359 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKGSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKAEAAAKE AAAKEAAAKE AAAKALEAEA AAKEAAAKEA AAKEAAAKAL EVLFQGPME ERRPHLDARP RNSHTNHRGP VDGELPPRAR NQANNPPANA LRGGASHPGR HPRANNHPAA YWQREERFRA M GRNPHQGR ...String:
MKGSAWSHPQ FEKGGGSGGG SGGSAWSHPQ FEKAEAAAKE AAAKEAAAKE AAAKALEAEA AAKEAAAKEA AAKEAAAKAL EVLFQGPME ERRPHLDARP RNSHTNHRGP VDGELPPRAR NQANNPPANA LRGGASHPGR HPRANNHPAA YWQREERFRA M GRNPHQGR RNQEGHASDE ARDQRHDQEN DTRWRNGNQD CRNRRPPWSN DNFQQWRTPH QKPTEQPQQA KKLGYKFLES LL QKDPSEV VITLATSLGL KELLSHSSMK SNFLELICQV LRKACSSKMD RQSVLHVLGI LKNSKFLKVC LPAYVVGMIT EPI PDIRNQ YPEHISNIIS LLQDLVSVFP ASSVQETSML VSLLPTSLNA LRASGVDIEE ETEKNLEKVQ TIIEHLQEKR REGT LRVDT YTLVQPEAED HVESYRTMPI YPTYNEVHLD ERPFLRPNII SGKYDSTAIY LDTHFRLLRE DFVRPLREGI LELLQ SFED QGLRKRKFDD IRIYFDTRII TPMCSSSGIV YKVQFDTKPL KFVRWQNSKR LLYGSLVCMS KDNFETFLFA TVSNRE QED LCRGIVQLCF NEQSQQLLAE VQPSDSFLMV ETTAYFEAYR HVLEGLQEVQ EEDVPFQRNI VECNSHVKEP RYLLMGG RY DFTPLIENPS ATGEFLRNVE GLRHPRINVL DPGQWPSKEA LKLDDSQMEA LQFALTRELA IIQGPPGTGK TYVGLKIV Q ALLTNESVWQ ISLQKFPILV VCYTNHALDQ FLEGIYNCQK TSIVRVGGRS NSEILKQFTL RELRNKREFR RNLPMHLRR AYMSIMTQMK ESEQELHEGA KTLECTMRGV LREQYLQKYI SPQHWESLMN GPVQDSEWIC FQHWKHSMML EWLGLGVGSF TQSVSPAGP ENTAQAEGDE EEEGEEESSL IEIAEEADLI QADRVIEEEE VVRPQRRKKE ESGADQELAK MLLAMRLDHC G TGTAAGQE QATGEWQTQR NQKKKMKKRV KDELRKLNTM TAAEANEIED VWQLDLSSRW QLYRLWLQLY QADTRRKILS YE RQYRTSA ERMAELRLQE DLHILKDAQV VGMTTTGAAK YRQILQKVEP RIVIVEEAAE VLEAHTIATL SKACQHLILI GDH QQLRPS ANVYDLAKNF NLEVSLFERL VKVNIPFVRL NYQHRMCPEI ARLLTPHIYQ DLENHPSVLK YEKIKGVSSN LFFV EHNFP EQEIQEGKSH QNQHEAHFVV ELCKYFLCQE YLPSQITILT TYTGQLFCLR KLMPAKTFAG VRVHVVDKYQ GEEND IILL SLVRSNQEGK VGFLQISNRI CVALSRAKKG MYCIGNMQML AKVPLWSKII HTLRENNQIG PMLRLCCQNH PETHTL VSK ASDFQKVPEG GCSLPCEFRL GCGHVCTRAC HPYDSSHKEF QCMKPCQKVI CQEGHRCPLV CFQECQPCQV KVPKTIP RC GHEQMVPCS

UniProtKB: NFX1-type zinc finger-containing protein 1

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 5 / 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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k 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: 3.5 µm / Nominal defocus min: 1.0 µm
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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57389
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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