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 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/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 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] Faculty of Pharmaceutical Sciences, University of Toyama; 2630, Sugitani, Toyama 930-0194, Japan [2] Graduate School of Innovative Life Science, University of Toyama; 2630, Sugitani, Toyama 930-0194, Japan [3].


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
THIOREDOXIN-LIKE PROTEIN 4A
A, C, E, G
142Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P83876 (Homo sapiens)
Explore P83876 
Go to UniProtKB:  P83876
PHAROS:  P83876
GTEx:  ENSG00000141759 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP83876
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
POLYGLUTAMINE-BINDING PROTEIN 1
B, D, F, H
43Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O60828 (Homo sapiens)
Explore O60828 
Go to UniProtKB:  O60828
PHAROS:  O60828
GTEx:  ENSG00000102103 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60828
Sequence Annotations
Expand
  • 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

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-30
    Type: Initial release
  • Version 1.1: 2014-05-14
    Changes: Database references
  • Version 1.2: 2023-12-20
    Changes: Data collection, Database references, Other, Refinement description