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: 2.40 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 

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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
  • Primary Citation of Related Structures:  
    1XK5

  • 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. Subsequently, the m7G-cap is hypermethylated to the 2,2,7-trimethylguanosine (m3G)-cap ...

    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 D Biol Crystallogr 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
snurportin-1A204Homo sapiensMutation(s): 0 
Gene Names: SNUPNRNUT1SPN1
UniProt & NIH Common Fund Data Resources
Find proteins for O95149 (Homo sapiens)
Explore O95149 
Go to UniProtKB:  O95149
PHAROS:  O95149
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TPG (Subject of Investigation/LOI)
Query on TPG

Download Ideal Coordinates CCD File 
B [auth A]2,2,7-TRIMETHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
C23 H35 N10 O18 P3
QBEUSSFUVVPDGT-NAGRZYTCSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TPG Binding MOAD:  1XK5 Kd: 1000 (nM) from 1 assay(s)
PDBBind:  1XK5 Kd: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.227 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.47α = 90
b = 57.47β = 90
c = 130.09γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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