Crystal structure of DEAD-box RNA helicase DDX3X at pre-unwound state

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

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The mechanism of RNA duplex recognition and unwinding by DEAD-box helicase DDX3X.

Song, H.Ji, X.

(2019) Nat Commun 10: 3085-3085

  • DOI: https://doi.org/10.1038/s41467-019-11083-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    DEAD-box helicases (DDXs) regulate RNA processing and metabolism by unwinding short double-stranded (ds) RNAs. Sharing a helicase core composed of two RecA-like domains (D1D2), DDXs function in an ATP-dependent, non-processive manner. As an attractive target for cancer and AIDS treatment, DDX3X and its orthologs are extensively studied, yielding a wealth of biochemical and biophysical data, including structures of apo-D1D2 and post-unwound D1D2:single-stranded RNA complex, and the structure of a D2:dsRNA complex that is thought to represent a pre-unwound state. However, the structure of a pre-unwound D1D2:dsRNA complex remains elusive, and thus, the mechanism of DDX action is not fully understood. Here, we describe the structure of a D1D2 core in complex with a 23-base pair dsRNA at pre-unwound state, revealing that two DDXs recognize a 2-turn dsRNA, each DDX mainly recognizes a single RNA strand, and conformational changes induced by ATP binding unwinds the RNA duplex in a cooperative manner.

  • Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD, 21702, USA. jix@mail.nih.gov.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase DDX3X
A, B
476Homo sapiensMutation(s): 0 
Gene Names: DDX3XDBXDDX3
UniProt & NIH Common Fund Data Resources
Find proteins for O00571 (Homo sapiens)
Explore O00571 
Go to UniProtKB:  O00571
PHAROS:  O00571
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00571
Sequence Annotations
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
C, D
28synthetic construct
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.102α = 90
b = 66.102β = 90
c = 230.463γ = 120
Software Package:
Software NamePurpose
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description