4IN0

Crystal Structure of human splicing factor dim2/TXNL4B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

High-resolution crystal structure of human Dim2/TXNL4B.

Jin, T.Guo, F.Wang, Y.Zhang, Y.

(2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 223-227

  • DOI: https://doi.org/10.1107/S1744309113000973
  • Primary Citation of Related Structures:  
    4IN0

  • PubMed Abstract: 

    TXNL4A (thioredoxin-like 4A) is an essential protein conserved from yeast to humans and is a component of the pre-mRNA splicing machinery. TXNL4B was identified as a TXNL4-family protein that also interacts with Prp6, an integral component of the U4/U6·U5 tri-snRNP complex, and has been shown to function in pre-mRNA splicing. A crystal structure of TXNL4B was determined at 1.33 Å resolution and refined to an Rwork of 0.13 and an Rfree of 0.18 with one native dimer in the asymmetric unit. Residues 1-33 of TXNL4B have previously been reported to be responsible for its interaction with Prp6. However, this region extends to the β-sheet core of the thioredoxin-fold structure of TXNL4B. This suggests that the interpretation of the previously reported GST pull-down results without considering the structure and stability of TXNL4B is debatable.


  • Organizational Affiliation

    Department of Biological and Chemical Sciences, Illinois Institute of Technology, 3101 South Dearborn Street, Chicago, IL 60616, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin-like protein 4B
A, B
148Homo sapiensMutation(s): 0 
Gene Names: DIM2DLPTXNL4B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NX01 (Homo sapiens)
Explore Q9NX01 
Go to UniProtKB:  Q9NX01
PHAROS:  Q9NX01
GTEx:  ENSG00000140830 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NX01
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G05551OP
GlyCosmos:  G05551OP
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.33 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.128 
  • R-Value Observed: 0.130 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.325α = 90
b = 63.64β = 92.29
c = 51.148γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Advisory, Refinement description
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-09-20
    Changes: Advisory, Data collection, Database references, Refinement description, Structure summary