9E2C | pdb_00009e2c

Crystal structure of DEAD-box RNA helicase DDX3X R326H mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.244 (Depositor), 0.247 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9E2C

This is version 1.1 of the entry. See complete history

Literature

DDX3X is a Cl - -sensitive RNA helicase.

Rosa E Silva, I.do Prado, P.F.V.Benevenutti, F.Z.de Oliveira, R.R.Passos, A.R.Canateli, C.Messias, I.G.Trindade, D.M.Bortot, L.O.Guerra, J.V.S.Hancio, T.Sforca, M.L.Nascimento, A.F.Z.Mercaldi, G.F.Pereira, J.G.C.Fonseca, M.C.de Oliveira, P.S.L.de Carvalho, M.Smetana, J.H.C.Krepischi, A.C.V.Franchini, K.G.de Oliveira, J.F.

(2026) Sci Signal 19: eadv4376-eadv4376

  • DOI: https://doi.org/10.1126/scisignal.adv4376
  • Primary Citation Related Structures: 
    9E2C

  • PubMed Abstract: 

    Cl - homeostasis is pivotal during neurodevelopment and in multiple processes in mature neurons, and its disruption is implicated in several neurodevelopmental disorders. Here, we investigated the role of Cl - in regulating DDX3X, an ATP-dependent RNA helicase that is associated with a neurodevelopmental disorder and is involved in stress granule assembly through biomolecular condensation. Cl - directly interacted with the DDX3X helicase core in the RNA binding region. This interaction impaired both ATPase and RNA helicase activities at physiologically relevant concentrations in a manner similar to inorganic phosphate and disrupted its condensation propensity in vitro. In neuroblastoma cells, Cl - efflux induced the formation of large, persistent DDX3X-containing stress granules. Furthermore, the R326H mutation, which is linked to a severe neurodevelopmental disorder, altered the chemical environment of the Cl - -binding site and impaired Cl - -sensitive functions. Together, our findings demonstrate that Cl - binding regulates DDX3X functions and provide insights into the molecular pathophysiology of a neurodevelopmental disorder-linked mutation in DDX3X.


  • Organizational Affiliation
    • Brazilian Biosciences National Laboratory (LNBio), Center for Research in Energy and Materials (CNPEM), 13083-970, Campinas, Brazil.

Macromolecule Content 

  • Total Structure Weight: 56.16 kDa 
  • Atom Count: 3,460 
  • Modeled Residue Count: 427 
  • Deposited Residue Count: 498 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Isoform 2 of ATP-dependent RNA helicase DDX3X498Homo sapiensMutation(s): 1 
Gene Names: DDX3XDBXDDX3
EC: 3.6.4.13
UniProt & NIH Common Fund Data Resources
Find proteins for O00571 (Homo sapiens)
Explore O00571 
Go to UniProtKB:  O00571
PHAROS:  O00571
GTEx:  ENSG00000215301 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00571
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.244 (Depositor), 0.247 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.212 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.347α = 90
b = 99.101β = 90
c = 105.351γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2022/12010-0
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil407904/2023-9

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2026-05-13
    Changes: Database references