1XBS

Crystal structure of human dim2: a dim1-like protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Biochemical Characterization and Crystal Structure of a Dim1 Family Associated Protein: Dim2

Simeoni, F.Arvai, A.Bello, P.Gondeau, C.Hopfner, K.-P.Neyroz, P.Heitz, F.Tainer, J.Divita, G.

(2005) Biochemistry 44: 11997-12008

  • DOI: 10.1021/bi050427o

  • PubMed Abstract: 
  • The U4/U6*U5 tri-snRNP complex is the catalytic core of the pre-mRNA splicing machinery. The thioredoxin-like protein hDim1 (U5-15 kDa) constitutes an essential component of the U5 particle, and its functions have been reported to be highly conserved ...

    The U4/U6*U5 tri-snRNP complex is the catalytic core of the pre-mRNA splicing machinery. The thioredoxin-like protein hDim1 (U5-15 kDa) constitutes an essential component of the U5 particle, and its functions have been reported to be highly conserved throughout evolution. Recently, the Dim1-like protein (DLP) family has been extended to other proteins harboring similar sequence motifs. Here we report the biochemical characterization and crystallographic structure of a 149 amino acid protein, hDim2, which shares 38% sequence identity with hDim1. The crystallographic structure of hDim2 solved at 2.5 A reveals a classical thioredoxin-fold structure. However, despite the similarity in the thioredoxin fold, hDim2 differs from hDim1 in many significant features. The structure of hDim2 contains an extra alpha helix (alpha3) and a beta strand (beta5), which stabilize the protein, suggesting that they may be involved in interactions with hDim2-specific partners. The stability and thermodynamic parameters of hDim2 were evaluated by combining circular dichroism and fluorescence spectroscopy together with chromatographic and cross-linking approaches. We have demonstrated that, in contrast to hDim1, hDim2 forms stable homodimers. The dimer interface is essentially stabilized by electrostatic interactions and involves tyrosine residues located in the alpha3 helix. Structural analysis reveals that hDim2 lacks some of the essential structural motifs and residues that are required for the biological activity and interactive properties of hDim1. Therefore, on the basis of structural investigations we suggest that, in higher eukaryotes, although both hDim1 and hDim2 are involved in pre-mRNA splicing, the two proteins are likely to participate in different multisubunit complexes and biological processes.


    Organizational Affiliation

    Department of Molecular Biophysics and Therapeutics, Centre de Recherches de Biochimie Macromoléculaire, FRE-2593 CNRS, 1919 Route de Mende, 34293 Montpellier, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Dim1-like protein
A
149Homo sapiensMutation(s): 0 
Gene Names: TXNL4B (DIM2, DLP)
Find proteins for Q9NX01 (Homo sapiens)
Go to Gene View: TXNL4B
Go to UniProtKB:  Q9NX01
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.242 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.160α = 90.00
b = 78.160β = 90.00
c = 60.334γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
AMoREphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description