6O16

Crystal structure of murine DHX37 in complex with RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.270 
  • R-Value Observed: 0.272 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis.

Boneberg, F.M.Brandmann, T.Kobel, L.van den Heuvel, J.Bargsten, K.Bammert, L.Kutay, U.Jinek, M.

(2019) RNA 25: 685-701

  • DOI: 10.1261/rna.069609.118
  • Primary Citation of Related Structures:  
    6O16

  • PubMed Abstract: 
  • Eukaryotic ribosome biogenesis is a highly orchestrated process involving numerous assembly factors including ATP-dependent RNA helicases. The DEAH helicase DHX37 (Dhr1 in yeast) is activated by the ribosome biogenesis factor UTP14A to facilitate maturation of the small ribosomal subunit ...

    Eukaryotic ribosome biogenesis is a highly orchestrated process involving numerous assembly factors including ATP-dependent RNA helicases. The DEAH helicase DHX37 (Dhr1 in yeast) is activated by the ribosome biogenesis factor UTP14A to facilitate maturation of the small ribosomal subunit. We report the crystal structure of DHX37 in complex with single-stranded RNA, revealing a canonical DEAH ATPase/helicase architecture complemented by a structurally unique carboxy-terminal domain (CTD). Structural comparisons of the nucleotide-free DHX37-RNA complex with DEAH helicases bound to RNA and ATP analogs reveal conformational changes resulting in a register shift in the bound RNA, suggesting a mechanism for ATP-dependent 3'-5' RNA translocation. We further show that a conserved sequence motif in UTP14A interacts with and activates DHX37 by stimulating its ATPase activity and enhancing RNA binding. In turn, the CTD of DHX37 is required, but not sufficient, for interaction with UTP14A in vitro and is essential for ribosome biogenesis in vivo. Together, these results shed light on the mechanism of DHX37 and the function of UTP14A in controlling its recruitment and activity during ribosome biogenesis.


    Organizational Affiliation

    Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DEAH (Asp-Glu-Ala-His) box polypeptide 37A, B975Mus musculusMutation(s): 0 
Gene Names: Dhx37
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NZL1 (Mus musculus)
Explore Q6NZL1 
Go to UniProtKB:  Q6NZL1
IMPC:  MGI:3028576
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3')C, D10synthetic construct
    Protein Feature View
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    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.88 Å
    • R-Value Free: 0.295 
    • R-Value Work: 0.270 
    • R-Value Observed: 0.272 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 83.829α = 90
    b = 137.593β = 93.34
    c = 94.225γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    XDSdata scaling
    PHENIXphasing

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Swiss National Science FoundationSwitzerlandNCCR RNA & Disease

    Revision History  (Full details and data files)

    • Version 1.0: 2019-04-17
      Type: Initial release
    • Version 1.1: 2019-05-29
      Changes: Data collection, Database references