Human DEAD-BOX RNA helicase DDX5 (P68), conserved domain I in complex with ADP

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

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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: e12791-e12791

  • 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 DDX5
A, B
242Homo sapiensMutation(s): 0 
Gene Names: DDX5G17P1HELRHLR1
EC: 3.6.1 (PDB Primary Data), (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P17844 (Homo sapiens)
Explore P17844 
Go to UniProtKB:  P17844
PHAROS:  P17844
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17844
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.57α = 90
b = 106.87β = 90
c = 117.32γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description