4BWS

Crystal structure of the heterotrimer of PQBP1, U5-15kD and U5-52kD.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

Starting Model: experimental
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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, D
142Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P83876 (Homo sapiens)
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Go to UniProtKB:  P83876
PHAROS:  P83876
GTEx:  ENSG00000141759 
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UniProt GroupP83876
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
POLYGLUTAMINE-BINDING PROTEIN 1
B, E
37Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O60828 (Homo sapiens)
Explore O60828 
Go to UniProtKB:  O60828
GTEx:  ENSG00000102103 
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UniProt GroupO60828
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CD2 ANTIGEN CYTOPLASMIC TAIL-BINDING PROTEIN 2
C, F
71Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O95400 (Homo sapiens)
Explore O95400 
Go to UniProtKB:  O95400
GTEx:  ENSG00000169217 
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UniProt GroupO95400
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.18α = 90
b = 40.47β = 95.92
c = 168.171γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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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