1XK5

Crystal structure of the m3G-cap-binding domain of snurportin1 in complex with a m3GpppG-cap dinucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for m(3)G-cap-mediated nuclear import of spliceosomal UsnRNPs by snurportin1

Strasser, A.Dickmanns, A.Luehrmann, R.Ficner, R.

(2005) Embo J. 24: 2235-2243

  • DOI: 10.1038/sj.emboj.7600701

  • PubMed Abstract: 
  • In higher eukaryotes the biogenesis of spliceosomal UsnRNPs involves a nucleocytoplasmic shuttling cycle. After the m7G-cap-dependent export of the snRNAs U1, U2, U4 and U5 to the cytoplasm, each of these snRNAs associates with seven Sm proteins. Sub ...

    In higher eukaryotes the biogenesis of spliceosomal UsnRNPs involves a nucleocytoplasmic shuttling cycle. After the m7G-cap-dependent export of the snRNAs U1, U2, U4 and U5 to the cytoplasm, each of these snRNAs associates with seven Sm proteins. Subsequently, the m7G-cap is hypermethylated to the 2,2,7-trimethylguanosine (m3G)-cap. The import adaptor snurportin1 recognises the m3G-cap and facilitates the nuclear import of the UsnRNPs by binding to importin-beta. Here we report the crystal structure of the m3G-cap-binding domain of snurportin1 with bound m3GpppG at 2.4 A resolution, revealing a structural similarity to the mRNA-guanyly-transferase. Snurportin1 binds both the hypermethylated cap and the first nucleotide of the RNA in a stacked conformation. This binding mode differs significantly from that of the m7G-cap-binding proteins Cap-binding protein 20 (CBP20), eukaryotic initiation factor 4E (eIF4E) and viral protein 39 (VP39). The specificity of the m3G-cap recognition by snurportin1 was evaluated by fluorescence spectroscopy, demonstrating the importance of a highly solvent exposed tryptophan for the discrimination of m7G-capped RNAs. The critical role of this tryptophan and as well of a tryptophan continuing the RNA base stack was confirmed by nuclear import assays and cap-binding activity tests using several snurportin1 mutants.


    Related Citations: 
    • Purification, crystallization and preliminary crystallographic data of the m3G cap-binding domain of human snRNP import factor snurportin 1
      Strasser, A.,Dickmanns, A.,Schmidt, U.,Penka, E.,Urlaub, H.,Sekine, M.,Luehrmann, R.,Ficner, R.
      (2004) ACTA CRYSTALLOGR.,SECT.D 60: 1628
    • Snurportin1, an m3G-cap-specific nuclear import receptor with a novel domain structure
      Huber, J.,Cronshagen, U.,Kadokura, M.,Marshallsay, C.,Wada, T.,Sekine, M.,Luehrmann, R.
      (1998) Embo J. 17: 4114


    Organizational Affiliation

    Department of Molecular Structural Biology, Institute for Microbiology and Genetics, University Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
snurportin-1
A
204Homo sapiensMutation(s): 0 
Gene Names: SNUPN (RNUT1, SPN1)
Find proteins for O95149 (Homo sapiens)
Go to Gene View: SNUPN
Go to UniProtKB:  O95149
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPG
Query on TPG

Download SDF File 
Download CCD File 
A
2,2,7-TRIMETHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
C23 H35 N10 O18 P3
QBEUSSFUVVPDGT-NAGRZYTCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TPGKd: 1240 nM BINDINGMOAD
TPGKd: 1000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 57.470α = 90.00
b = 57.470β = 90.00
c = 130.090γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SHARPphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-06-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance