Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.15 kDa 
• Atom Count: 2844 
• Residue Count: 282 
• Unique protein chains: 1

4IN0

Crystal Structure of human splicing factor dim2/TXNL4B

• DOI: 10.2210/pdb4IN0/pdb

• Classification: SPLICING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-01-03 Released: 2013-03-13 
• Deposition Author(s): Jin, T.C., Guo, F., Zhang, Y.Z.

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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 

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

• PubMed: 23519793 
• 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·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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin-like protein 4B	A, B	148	Homo sapiens	Mutation(s): 0  Gene Names: DIM2, DLP, TXNL4B
Find proteins for Q9NX01 (Homo sapiens) Explore Q9NX01  Go to UniProtKB:  Q9NX01
NIH Common Fund Data Resources
PHAROS:  Q9NX01 GTEx:  ENSG00000140830

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose	C	2		N/A

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900003	C	sucrose	Oligosaccharide /  Nutrient		--

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 = 39.325	α = 90
b = 63.64	β = 92.29
c = 51.148	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-01-03 
• Released Date: 2013-03-13 
Deposition Author(s): Jin, T.C., Guo, F., Zhang, Y.Z.

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