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 

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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: 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·U ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thioredoxin-like protein 4B AB148Homo sapiensMutation(s): 0 
Gene Names: DIM2DLPTXNL4B
Find proteins for Q9NX01 (Homo sapiens)
Explore Q9NX01 
Go to UniProtKB:  Q9NX01
NIH Common Fund Data Resources
PHAROS:  Q9NX01
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
C
2 N/A Oligosaccharides Interaction
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003
CsucroseOligosaccharide /  Nutrient

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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 

  • 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