Human DEAD-box RNA helicase DDX20, Conserved domain I (DEAD) in complex with AMPPNP (Adenosine-(Beta,gamma)-imidotriphosphate)

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Comparative Structural Analysis of Human DEAD-Box RNA Helicases.

Schutz, P.Karlberg, T.van den Berg, S.Collins, R.Lehtio, L.Hogbom, M.Holmberg-Schiavone, L.Tempel, W.Park, H.W.Hammarstrom, M.Moche, M.Thorsell, A.G.Schuler, H.

(2010) PLoS One 5: 12791-12791

  • DOI: https://doi.org/10.1371/journal.pone.0012791
  • Primary Citation of Related Structures:  
    2G9N, 2P6N, 2PL3, 2RB4, 3B7G, 3BER, 3BOR, 3DKP, 3FE2, 3IUY, 3LY5

  • PubMed Abstract: 

    DEAD-box RNA helicases play various, often critical, roles in all processes where RNAs are involved. Members of this family of proteins are linked to human disease, including cancer and viral infections. DEAD-box proteins contain two conserved domains that both contribute to RNA and ATP binding. Despite recent advances the molecular details of how these enzymes convert chemical energy into RNA remodeling is unknown. We present crystal structures of the isolated DEAD-domains of human DDX2A/eIF4A1, DDX2B/eIF4A2, DDX5, DDX10/DBP4, DDX18/myc-regulated DEAD-box protein, DDX20, DDX47, DDX52/ROK1, and DDX53/CAGE, and of the helicase domains of DDX25 and DDX41. Together with prior knowledge this enables a family-wide comparative structural analysis. We propose a general mechanism for opening of the RNA binding site. This analysis also provides insights into the diversity of DExD/H- proteins, with implications for understanding the functions of individual family members.

  • Organizational Affiliation

    Structural Genomics Consortium, Karolinska Institutet, Stockholm, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable ATP-dependent RNA helicase DDX20
A, B
230Homo sapiensMutation(s): 0 
Gene Names: DDX20DP103GEMIN3
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHI6 (Homo sapiens)
Explore Q9UHI6 
Go to UniProtKB:  Q9UHI6
GTEx:  ENSG00000064703 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHI6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on ANP

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
C10 H17 N6 O12 P3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.56α = 90
b = 63.56β = 90
c = 214.6γ = 120
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2007-11-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description