Crystal structure of the DDX41 DEAD domain in an apo closed form

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

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Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide

Omura, H.Oikawa, D.Nakane, T.Kato, M.Ishii, R.Ishitani, R.Tokunaga, F.Nureki, O.

(2016) Sci Rep 6: 34756-34756

  • DOI: https://doi.org/10.1038/srep34756
  • Primary Citation of Related Structures:  
    5GVR, 5GVS

  • PubMed Abstract: 

    In the innate immune system, pattern recognition receptors (PRRs) specifically recognize ligands derived from bacteria or viruses, to trigger the responsible downstream pathways. DEAD box protein 41 (DDX41) is an intracellular PRR that triggers the downstream pathway involving the adapter STING, the kinase TBK1, and the transcription factor IRF3, to activate the type I interferon response. DDX41 is unique in that it recognizes two different ligands; i.e., double-stranded DNA (dsDNA) and cyclic dinucleotides (CDN), via its DEAD domain. However, the structural basis for the ligand recognition by the DDX41 DEAD domain has remained elusive. Here, we report two crystal structures of the DDX41 DEAD domain in apo forms, at 1.5 and 2.2 Å resolutions. A comparison of the two crystal structures revealed the flexibility in the ATP binding site, suggesting its formation upon ATP binding. Structure-guided functional analyses in vitro and in vivo demonstrated the overlapped binding surface for dsDNA and CDN, which is distinct from the ATP-binding site. We propose that the structural rearrangement of the ATP binding site is crucial for the release of ADP, enabling the fast turnover of DDX41 for the dsDNA/CDN-induced STING activation pathway.

  • Organizational Affiliation

    Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX41234Homo sapiensMutation(s): 0 
Gene Names: DDX41ABS
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJV9 (Homo sapiens)
Explore Q9UJV9 
Go to UniProtKB:  Q9UJV9
GTEx:  ENSG00000183258 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UJV9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LMR

Download Ideal Coordinates CCD File 
B [auth A](2S)-2-hydroxybutanedioic acid
C4 H6 O5
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.83α = 90
b = 81.83β = 90
c = 69.57γ = 120
Software Package:
Software NamePurpose
REFMACmodel building
XDSdata scaling
XDSdata reduction
XDSdata processing
XDSdata extraction
XDSdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description