Crystal structure of human DEAD-box RNA helicase DDX21 at apo state

Experimental Data Snapshot

  • Resolution: 3.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 

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This is version 1.3 of the entry. See complete history


Structural Basis of Human Helicase DDX21 in RNA Binding, Unwinding, and Antiviral Signal Activation.

Chen, Z.Li, Z.Hu, X.Xie, F.Kuang, S.Zhan, B.Gao, W.Chen, X.Gao, S.Li, Y.Wang, Y.Qian, F.Ding, C.Gan, J.Ji, C.Xu, X.Zhou, Z.Huang, J.He, H.H.Li, J.

(2020) Adv Sci (Weinh) 7: 2000532-2000532

  • DOI: https://doi.org/10.1002/advs.202000532
  • Primary Citation of Related Structures:  
    6L5L, 6L5M, 6L5N, 6L5O

  • PubMed Abstract: 

    RNA helicase DDX21 plays vital roles in ribosomal RNA biogenesis, transcription, and the regulation of host innate immunity during virus infection. How DDX21 recognizes and unwinds RNA and how DDX21 interacts with virus remain poorly understood. Here, crystal structures of human DDX21 determined in three distinct states are reported, including the apo-state, the AMPPNP plus single-stranded RNA (ssRNA) bound pre-hydrolysis state, and the ADP-bound post-hydrolysis state, revealing an open to closed conformational change upon RNA binding and unwinding. The core of the RNA unwinding machinery of DDX21 includes one wedge helix, one sensor motif V and the DEVD box, which links the binding pockets of ATP and ssRNA. The mutant D339H/E340G dramatically increases RNA binding activity. Moreover, Hill coefficient analysis reveals that DDX21 unwinds double-stranded RNA (dsRNA) in a cooperative manner. Besides, the nonstructural (NS1) protein of influenza A inhibits the ATPase and unwinding activity of DDX21 via small RNAs, which cooperatively assemble with DDX21 and NS1. The structures illustrate the dynamic process of ATP hydrolysis and RNA unwinding for RNA helicases, and the RNA modulated interaction between NS1 and DDX21 generates a fresh perspective toward the virus-host interface. It would benefit in developing therapeutics to combat the influenza virus infection.

  • Organizational Affiliation

    State Key Laboratory of Genetic Engineering Department of Neurology School of Life Sciences and Huashan Hospital Collaborative Innovation Center of Genetics and Development Engineering Research Center of Gene Technology of MOE Shanghai Engineering Research Center of Industrial Microorganisms Fudan University Shanghai 200438 China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleolar RNA helicase 2372Homo sapiensMutation(s): 0 
Gene Names: DDX21
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR30 (Homo sapiens)
Explore Q9NR30 
Go to UniProtKB:  Q9NR30
GTEx:  ENSG00000165732 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NR30
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MG

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 3.10 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.17α = 90
b = 46.63β = 101.16
c = 58.49γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-06-17
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Data collection
  • Version 1.2: 2020-08-12
    Changes: Database references
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references