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 32UL | pdb_000032ul

Structure of ZNFX1 in the ATP-bound, pre-ATP hydrolysis state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 32UL

This is version 1.1 of the entry. See complete history. 

Literature

ZNFX1, an immunoregulatory RNA helicase and E3 ubiquitin ligase, assembles into pleiomorphic polymers.

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.

(2026) Mol Cell 86: 4018-4031.e4

  • DOI: https://doi.org/10.1016/j.molcel.2026.09.002
  • Primary Citation Related Structures: 
    32UL, 32UM, 32UN

  • PubMed Abstract: 

    NFX1-type zinc-finger-containing 1 (ZNFX1) is an SF1-family RNA helicase essential for innate immunity. Patients with ZNFX1 mutations experience recurrent infections, yet the underlying mechanism remains unclear. We determined cryo-electron microscopy (cryo-EM) structures of RNA-bound and RNA-free ZNFX1 and revealed auto-inhibition of the helicase-associated ATPase through a regulatory insertion occluding the RNA-binding groove. ZNFX1 also functions as a bi-catalytic E3 ubiquitin ligase, containing an RZ finger homologous to RNF213 and a previously unidentified Miz-like domain, which cooperate in catalyzing ubiquitylation. Ubiquitin chains enhance E3 activity further. Patient mutations demonstrate that the helicase/ATPase, E3 ligase, and the rigid zinc-finger stalk connecting them are required for function. ZNFX1 can assemble into structured, pleiomorphic polymers fostering trans-auto-ubiquitylation; understanding this reveals a mechanism that controls ZNFX1 stability and may facilitate RNA sequestration in stress granules and antiviral activity. These findings establish ZNFX1 as a multifunctional enzyme in immunity that couples RNA sensing to ubiquitin signaling and assembles into higher-order structures for signal amplification.


  • Organizational Affiliation: 
    • Protein and Nucleic Acid Chemistry Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.

Macromolecule Content 

  • Total Structure Weight: 225.14 kDa 
  • Atom Count: 8,769 
  • Modeled Residue Count: 1,088 
  • Deposited Residue Count: 1,956 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NFX1-type zinc finger-containing protein 11,956Homo sapiensMutation(s): 0 
Gene Names: ZNFX1, KIAA1404
EC: 3.6.4 (PDB Primary Data), 2.3.2.27 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P2E3 (Homo sapiens)
Explore Q9P2E3 
Go to UniProtKB:  Q9P2E3
PHAROS:  Q9P2E3
GTEx:  ENSG00000124201 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P2E3
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION5.0

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--
UK Research and Innovation (UKRI)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-30
    Type: Initial release
  • Version 1.1: 2026-10-14
    Changes: Data collection, Database references