5GVS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

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: 10.1038/srep34756
  • Primary Citation of Related Structures:  
    5GVS, 5GVR

  • 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 d ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX41ABCD231Homo sapiensMutation(s): 0 
Gene Names: DDX41ABS
EC: 3.6.4.13
Find proteins for Q9UJV9 (Homo sapiens)
Explore Q9UJV9 
Go to UniProtKB:  Q9UJV9
NIH Common Fund Data Resources
PHAROS  Q9UJV9
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.211 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.188α = 90
b = 50.96β = 95.51
c = 202.599γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXmodel building
MOSFLMdata collection
MOSFLMdata extraction
MOSFLMdata processing
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan--

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Derived calculations