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- PDB-32um: Structure of ZNFX1 bound to RNA -

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Basic information

Entry
Database: PDB / ID: 32um
TitleStructure of ZNFX1 bound to RNA
Components
  • NFX1-type zinc finger-containing protein 1
  • RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')
KeywordsANTIVIRAL PROTEIN / ZNFX1 / RNA helicase / ubiquitin ligase / Zn fingers / armadillo repeat / dimer / ATPase / RNA / single-stranded RNA
Function / homology
Function and homology information


nuclear RNA-directed RNA polymerase complex / regulatory ncRNA-mediated heterochromatin formation / negative regulation of viral genome replication / helicase activity / activation of innate immune response / RING-type E3 ubiquitin transferase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule / defense response to virus / defense response to bacterium ...nuclear RNA-directed RNA polymerase complex / regulatory ncRNA-mediated heterochromatin formation / negative regulation of viral genome replication / helicase activity / activation of innate immune response / RING-type E3 ubiquitin transferase / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cytoplasmic stress granule / defense response to virus / defense response to bacterium / innate immune response / mitochondrial outer membrane / 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. / UPF1-type helicase core domain profile. / DNA2/NAM7 helicase, helicase domain / AAA domain ...: / ZNFX1 domain / Zinc finger, NF-X1-type / ZnF_NFX / Zinc finger, RZ-type / RZ type zinc finger domain / Zinc finger RZ-type profile. / UPF1-type helicase core domain 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
RNA / RNA (> 10) / NFX1-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsYip, M.C.J. / Naydenova, K. / Randow, F.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
UK Research and Innovation (UKRI) United Kingdom
CitationJournal: To Be Published
Title: ZNFX1, an immunoregulatory RNA helicase and E3 ubiquitin ligase, assembles into pleiomorphic polymers
Authors: Naydenova, K. / Mund, T. / Yip, M.C.J. / Harper, C.M. / Leigh, K.E. / Hankinson, J. / Boyle, K.B. / Heatley, A. / Otten, E.G. / Lulla, V. / Modis, Y. / Randow, F.
History
DepositionJul 26, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 30, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NFX1-type zinc finger-containing protein 1
G: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Theoretical massNumber of molelcules
Total (without water)227,9302
Polymers227,9302
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein NFX1-type zinc finger-containing protein 1 / ATP- dependent RNA translocase ZNFX1 / E3 ubiquitin-protein and -ssRNA ligase ZNFX1


Mass: 224607.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNFX1, KIAA1404 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9P2E3, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement, RING-type E3 ubiquitin transferase
#2: RNA chain RNA (5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')


Mass: 3322.866 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
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: Human ZNFX1 protein bound to RNA / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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: 37.3 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
5cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 134177 / Symmetry type: POINT
RefinementHighest resolution: 3.1 Å

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