Crystal structure of the N-terminal domain of rck/p54, a human DEAD-box protein

Experimental Data Snapshot

  • Resolution: 2.01 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 

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Structural insight of human DEAD-box protein rck/p54 into its substrate recognition with conformational changes

Matsui, T.Hogetsu, K.Usukura, J.Sato, T.Kumasaka, T.Akao, Y.Tanaka, N.

(2006) Genes Cells 11: 439-452

  • DOI: https://doi.org/10.1111/j.1365-2443.2006.00951.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Human rck/p54, a product of the gene cloned at the breakpoint of t(11; 14) (q23;q32) chromosomal translocation on 11q23 in B-cell lymphoma, is a member of the DEAD-box RNA helicase family. Here, the crystal structure of Nc-rck/p54, the N-terminal core domain of rck/p54, revealed that the P-loop in motif I formed a closed conformation, which was induced by Asn131, a residue unique to the RCK subfamily. It appears that ATP does not bind to the P-loop. The results of dynamic light scattering revealed to ATP-induced conformational change of rck/p54. It was demonstrated that free rck/p54 is a distended molecule in solution, and that the approach between N-terminal core and C-terminal domains for ATP binding would be essential when unwinding RNA. The results from helicase assay using electron micrograph, ATP hydrolytic and luciferase assay showed that c-myc IRES RNA, whose secondary structure regulates IRES-dependant translation, was unwound by rck/p54 and indicated that it is a good substrate for rck/p54. Over-expression of rck/p54 in HeLa cells caused growth inhibition and cell cycle arrest at G2/M with down-regulation of c-myc expression. These findings altogether suggest that rck/p54 may affect the IRES-dependent translation of c-myc even in the cells.

  • Organizational Affiliation

    Department of Life Science, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, 226-8501, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ATP-dependent RNA helicase p54
A, B
206Homo sapiensMutation(s): 0 
Gene Names: HUMRCK
UniProt & NIH Common Fund Data Resources
Find proteins for P26196 (Homo sapiens)
Explore P26196 
Go to UniProtKB:  P26196
PHAROS:  P26196
GTEx:  ENSG00000110367 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26196
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TLA

Download Ideal Coordinates CCD File 
C4 H6 O6
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Experimental Data & Validation

Experimental Data

  • Resolution: 2.01 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.52α = 90
b = 73.14β = 90
c = 84.79γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-04-13
    Type: Initial release
  • Version 1.1: 2008-04-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description