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 

wwPDB Validation   3D Report Full Report


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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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THIOREDOXIN-LIKE PROTEIN 4A AD142Homo sapiensMutation(s): 0 
Gene Names: TXNL4ADIM1TXNL4
Find proteins for P83876 (Homo sapiens)
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Go to UniProtKB:  P83876
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PHAROS:  P83876
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
POLYGLUTAMINE-BINDING PROTEIN 1 BE37Homo sapiensMutation(s): 0 
Gene Names: PQBP1NPW38JM26
Find proteins for O60828 (Homo sapiens)
Explore O60828 
Go to UniProtKB:  O60828
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PHAROS:  O60828
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CD2 ANTIGEN CYTOPLASMIC TAIL-BINDING PROTEIN 2 CF71Homo sapiensMutation(s): 0 
Gene Names: CD2BP2KIAA1178
Find proteins for O95400 (Homo sapiens)
Explore O95400 
Go to UniProtKB:  O95400
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PHAROS:  O95400
Protein Feature View
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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 

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