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- PDB-13fz: Cryo-EM structure of human ZNFX1 dimer in complex with ssRNA and ATPgS -

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Basic information

Entry
Database: PDB / ID: 13fz
TitleCryo-EM structure of human ZNFX1 dimer in complex with ssRNA and ATPgS
Components
  • NFX1-type zinc finger-containing protein 1
  • RNA
KeywordsRNA / RNA helicase / E3 Ligase
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 / innate immune response ...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 / innate immune response / defense response to bacterium / 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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / RNA / RNA (> 10) / NFX1-type zinc finger-containing protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsWang, F. / He, Q. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131754 United States
CitationJournal: Nat Commun / Year: 2026
Title: Cryo-EM structures of autoinhibited and RNA-activated ZNFX1 helicase
Authors: He, Q. / Wang, F. / Rassool, F.V. / Baylin, S.B. / Li, H.
History
DepositionMay 5, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 7, 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
B: RNA
C: NFX1-type zinc finger-containing protein 1
D: RNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)481,1136
Polymers480,0664
Non-polymers1,0462
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


Mass: 220537.000 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZNFX1, KIAA1404
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: Q9P2E3
#2: RNA chain RNA


Mass: 19496.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
Has ligand of interestY
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: ZNFX1 and ssRNA complex / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.4 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Mammalian expression vector Flag-MCS-pcDNA3.1 (others)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
225 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidHEPES1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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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: 1600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7.1particle selection
9PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 10642983
3D reconstructionResolution: 3.37 Å / Resolution method: OTHER / Num. of particles: 263896 / Symmetry type: POINT
RefinementHighest resolution: 3.37 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00419656
ELECTRON MICROSCOPYf_angle_d0.72526686
ELECTRON MICROSCOPYf_dihedral_angle_d11.3642931
ELECTRON MICROSCOPYf_chiral_restr0.0442992
ELECTRON MICROSCOPYf_plane_restr0.0053332

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