4N0T

Core structure of the U6 small nuclear ribonucleoprotein at 1.7 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Core structure of the U6 small nuclear ribonucleoprotein at 1.7- angstrom resolution.

Montemayor, E.J.Curran, E.C.Liao, H.H.Andrews, K.L.Treba, C.N.Butcher, S.E.Brow, D.A.

(2014) Nat Struct Mol Biol 21: 544-551

  • DOI: https://doi.org/10.1038/nsmb.2832
  • Primary Citation of Related Structures:  
    4N0T

  • PubMed Abstract: 

    The spliceosome is a dynamic assembly of five small nuclear ribonucleoproteins (snRNPs) that removes introns from eukaryotic pre-mRNA. U6, the most conserved of the spliceosomal small nuclear RNAs (snRNAs), participates directly in catalysis. Here, we report the crystal structure of the Saccharomyces cerevisiae U6 snRNP core containing most of the U6 snRNA and all four RRM domains of the Prp24 protein. It reveals a unique interlocked RNP architecture that sequesters the 5' splice site-binding bases of U6 snRNA. RRMs 1, 2 and 4 of Prp24 form an electropositive groove that binds double-stranded RNA and may nucleate annealing of U4 and U6 snRNAs. Substitutions in Prp24 that suppress a mutation in U6 localize to direct RNA-protein contacts. Our results provide the most comprehensive view to date of a multi-RRM protein bound to RNA and reveal striking coevolution of protein and RNA structure.


  • Organizational Affiliation

    1] Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA. [2] Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U4/U6 snRNA-associated-splicing factor PRP24374Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PRP24YM8156.10CYMR268C
UniProt
Find proteins for P49960 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P49960 
Go to UniProtKB:  P49960
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49960
Sequence Annotations
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  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains LengthOrganismImage
U6 snRNA72N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.782α = 90
b = 71.37β = 109.62
c = 82.081γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-07-02
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description