4B3G

crystal structure of Ighmbp2 helicase in complex with RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Ighmbp2 Helicase Structure Reveals the Molecular Basis for Disease-Causing Mutations in Dmsa1.

Lim, S.C.Bowler, M.W.Lai, T.F.Song, H.

(2012) Nucleic Acids Res 40: 11009

  • DOI: 10.1093/nar/gks792
  • Primary Citation of Related Structures:  
    4B3F, 4B3G

  • PubMed Abstract: 
  • Mutations in immunoglobulin µ-binding protein 2 (Ighmbp2) cause distal spinal muscular atrophy type 1 (DSMA1), an autosomal recessive disease that is clinically characterized by distal limb weakness and respiratory distress. However, despite extensive studies, the mechanism of disease-causing mutations remains elusive ...

    Mutations in immunoglobulin µ-binding protein 2 (Ighmbp2) cause distal spinal muscular atrophy type 1 (DSMA1), an autosomal recessive disease that is clinically characterized by distal limb weakness and respiratory distress. However, despite extensive studies, the mechanism of disease-causing mutations remains elusive. Here we report the crystal structures of the Ighmbp2 helicase core with and without bound RNA. The structures show that the overall fold of Ighmbp2 is very similar to that of Upf1, a key helicase involved in nonsense-mediated mRNA decay. Similar to Upf1, domains 1B and 1C of Ighmbp2 undergo large conformational changes in response to RNA binding, rotating 30° and 10°, respectively. The RNA binding and ATPase activities of Ighmbp2 are further enhanced by the R3H domain, located just downstream of the helicase core. Mapping of the pathogenic mutations of DSMA1 onto the helicase core structure provides a molecular basis for understanding the disease-causing consequences of Ighmbp2 mutations.


    Organizational Affiliation

    Institute of Molecular and Cell Biology, Proteos, Singapore 138673, Singapore.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-BINDING PROTEIN SMUBP-2A, B646Homo sapiensMutation(s): 0 
Gene Names: IGHMBP2SMBP2SMUBP2
EC: 3.6.4.12 (PDB Primary Data), 3.6.4.13 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P38935 (Homo sapiens)
Explore P38935 
Go to UniProtKB:  P38935
PHAROS:  P38935
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    RNA (5'-(AP*AP*AP*AP*AP*AP*AP*AP*AP)-3')C [auth G], D [auth H]9N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.85 Å
    • R-Value Free: 0.292 
    • R-Value Work: 0.206 
    • R-Value Observed: 0.211 
    • Space Group: P 31 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 87.288α = 90
    b = 87.288β = 90
    c = 372.692γ = 120
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    XDSdata reduction
    SCALAdata scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    • Deposited Date: 2012-07-24 
    • Released Date: 2012-09-26 
    • Deposition Author(s): Lim, S.C., Song, H.

    Revision History  (Full details and data files)

    • Version 1.0: 2012-09-26
      Type: Initial release
    • Version 1.1: 2012-12-19
      Changes: Database references