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- PDB-9eve: Crystal structure of the ARM domain of human ZNFX1 -

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Basic information

Entry
Database: PDB / ID: 9eve
TitleCrystal structure of the ARM domain of human ZNFX1
ComponentsNFX1-type zinc finger-containing protein 1
KeywordsRNA BINDING PROTEIN / Helicase / E3 ligase / armadillo domain
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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.67 Å
AuthorsGrabarczyk, D.B. / Deszcz, L. / Clausen, T.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
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
DepositionMar 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 3, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Sep 10, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NFX1-type zinc finger-containing protein 1
B: NFX1-type zinc finger-containing protein 1


Theoretical massNumber of molelcules
Total (without water)44,9262
Polymers44,9262
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.850, 51.570, 86.650
Angle α, β, γ (deg.)90.000, 101.746, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1chain "B"

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: GLU / End label comp-ID: GLU / Auth seq-ID: 17 - 189 / Label seq-ID: 17 - 189

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (0.909738830297, -0.0293364556705, 0.414143251808), (-0.0317716052761, -0.999494646069, -0.00100875084877), (0.413963556062, -0.012240296107, -0.910211156493)Vector: -9. ...NCS oper: (Code: given
Matrix: (0.909738830297, -0.0293364556705, 0.414143251808), (-0.0317716052761, -0.999494646069, -0.00100875084877), (0.413963556062, -0.012240296107, -0.910211156493)
Vector: -9.15069227013, -0.287125859414, 42.2222612432)

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Components

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


Mass: 22463.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNFX1, KIAA1404 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9P2E3
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, NaCl, citrate pH 4.2, glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 20, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 3.67→51.57 Å / Num. obs: 4452 / % possible obs: 97.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 66.91 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.026 / Rrim(I) all: 0.07 / Net I/σ(I): 17.6
Reflection shellResolution: 3.67→4.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 12 / Num. unique obs: 961 / CC1/2: 0.995 / % possible all: 89.8

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.67→44.3 Å / SU ML: 0.516 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.485
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2356 462 10.45 %
Rwork0.1978 3961 -
obs0.2019 4423 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 80.37 Å2
Refinement stepCycle: LAST / Resolution: 3.67→44.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 0 0 2698
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212732
X-RAY DIFFRACTIONf_angle_d0.48443686
X-RAY DIFFRACTIONf_chiral_restr0.0357454
X-RAY DIFFRACTIONf_plane_restr0.0043460
X-RAY DIFFRACTIONf_dihedral_angle_d13.29861058
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.398054491818 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.67-4.20.27041360.20381240X-RAY DIFFRACTION92.1
4.2-5.290.23641590.18521348X-RAY DIFFRACTION99.41
5.29-44.30.21581670.20471373X-RAY DIFFRACTION99.1

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