4BWQ

Crystal structure of U5-15kD in a complex with PQBP1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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This is version 1.1 of the entry. See complete history. 


Literature

Mutations in the Pqbp1 Gene Prevent its Interaction with the Spliceosomal Protein U5-15Kd.

Mizuguchi, M., Obita, T., Serita, T., Kojima, R., Nabeshima, Y., Okazawa, H.

(2014) Nat Commun 5: 3822

  • DOI: 10.1038/ncomms4822
  • Primary Citation of Related Structures:  
    4BWQ, 4BWS, 4CDO

  • PubMed Abstract: 

    • A loss-of-function of polyglutamine tract-binding protein 1 (PQBP1) induced by frameshift mutations is believed to cause X-linked mental retardation. However, the mechanism by which structural changes in PQBP1 lead to mental retardation is unknown. Here ...

    A loss-of-function of polyglutamine tract-binding protein 1 (PQBP1) induced by frameshift mutations is believed to cause X-linked mental retardation. However, the mechanism by which structural changes in PQBP1 lead to mental retardation is unknown. Here we present the crystal structure of a C-terminal fragment of PQBP1 in complex with the spliceosomal protein U5-15 kD. The U5-15 kD hydrophobic groove recognizes a YxxPxxVL motif in PQBP1, and mutations within this motif cause a loss-of-function phenotype of PQBP1 in vitro. The YxxPxxVL motif is absent in all PQBP1 frameshift mutants seen in cases of mental retardation. These results suggest a mechanism by which the loss of the YxxPxxVL motif could lead to the functional defects seen in this type of mental retardation.

    Organizational Affiliation: 

    1] Department of Neuropathology, Medical Research Institute, Tokyo Medical and Dental University; 1-5-45, Yushima, Bunkyo-ku, Tokyo 113-8510, Japan [2] Center for Brain Integration Research, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THIOREDOXIN-LIKE PROTEIN 4A A, C, E, G142Homo sapiensMutation(s): 0 
Gene Names: TXNL4A, DIM1, TXNL4
Find proteins for P83876 (Homo sapiens)
Explore P83876 
Go to UniProtKB:  P83876
NIH Common Fund Data Resources
PHAROS:  P83876
GTEx:  ENSG00000141759
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
POLYGLUTAMINE-BINDING PROTEIN 1 B, D, F, H43Homo sapiensMutation(s): 0 
Gene Names: PQBP1, NPW38, JM26
Find proteins for O60828 (Homo sapiens)
Explore O60828 
Go to UniProtKB:  O60828
NIH Common Fund Data Resources
PHAROS:  O60828
GTEx:  ENSG00000102103
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.22α = 90
b = 40.04β = 93.45
c = 118.77γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-30
    Type: Initial release
  • Version 1.1: 2014-05-14
    Changes: Database references