Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.81 kDa 
• Atom Count: 1194 
• Modelled Residue Count: 131 
• Deposited Residue Count: 142 
• Unique protein chains: 1

1QGV

HUMAN SPLICEOSOMAL PROTEIN U5-15KD

• PDB DOI: 10.2210/pdb1QGV/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-05-06 Released: 1999-12-12 
• Deposition Author(s): Reuter, K., Nottrott, S., Fabrizio, P., Luehrmann, R., Ficner, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.269 
• R-Value Work: 0.216 

Literature

Identification, characterization and crystal structure analysis of the human spliceosomal U5 snRNP-specific 15 kD protein.

Reuter, K., Nottrott, S., Fabrizio, P., Luhrmann, R., Ficner, R.

(1999) J Mol Biol 294: 515-525

• PubMed: 10610776 
• DOI: 10.1006/jmbi.1999.3258
• Primary Citation of Related Structures:  
  1QGV


• PubMed Abstract: 
  

The U5 small ribonucleoprotein particle (snRNP) contains various proteins involved in catalytic activities mediating conformational rearrangements of the spliceosome. We have isolated and characterized the evolutionarily highly conserved human U5 snRNP-specific protein U5-15kD. The crystal structure of U5-15kD determined at 1.4 A resolution revealed a thioredoxin-like fold and represents the first structure of a U5 snRNP-specific protein known so far. With respect to human thioredoxin the U5-15kD protein contains 37 additional residues causing structural changes which most likely form putative binding sites for other spliceosomal proteins or RNA. Moreover, a novel intramolecular disulfide bond replaces the canonical one found in the thioredoxin family. Even though U5-15kD appears to lack protein disulfide isomerase activity, it is strictly required for pre-mRNA splicing in vivo as we demonstrate by genetic depletion of its ortholog in Saccharomyces cerevisiae. Our data suggest that the previously reported involvement of its Schizosaccharomyces pombe ortholog Dim1p in cell cycle regulation is a consequence of its essential role in pre-mRNA splicing.

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Related Citations: 

• Overproduction, purification, crystallization and preliminary x-ray diffraction studies of the human spliceosomal protein U5-15kD.
  Reuter, K., Ficner, R.
  (1999) Acta Crystallogr D Biol Crystallogr 55: 888

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Organizational Affiliation: 

Institut für Molekularbiologie und Tumorforschung, Universität Marburg, 35037, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPLICEOSOMAL PROTEIN U5-15KD	A	142	Homo sapiens	Mutation(s): 0  Gene Names: U5-15KD, TXNL4A, DIM1, TXNL4
UniProt & NIH Common Fund Data Resources
Find proteins for P83876 (Homo sapiens) Explore P83876  Go to UniProtKB:  P83876
PHAROS:  P83876

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.269 
• R-Value Work: 0.216 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.225	α = 90
b = 65.092	β = 90
c = 36.275	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MLPHARE	phasing
SHARP	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-05-06 
• Released Date: 1999-12-12 
Deposition Author(s): Reuter, K., Nottrott, S., Fabrizio, P., Luehrmann, R., Ficner, R.

Revision History  

• Version 1.0: 1999-12-12
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-27
  Changes: Database references