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

Experimental Data Snapshot

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

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This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1038/sj.emboj.7600701
  • Primary Citation of Related Structures:  

  • 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. 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.

  • Organizational Affiliation

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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
snurportin-1204Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O95149 (Homo sapiens)
Explore O95149 
Go to UniProtKB:  O95149
GTEx:  ENSG00000169371 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95149
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TPG

Download Ideal Coordinates CCD File 
C23 H35 N10 O18 P3
Binding Affinity Annotations 
IDSourceBinding Affinity
TPG PDBBind:  1XK5 Kd: 1000 (nM) from 1 assay(s)
Binding MOAD:  1XK5 Kd: 1000 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • 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

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
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references, Derived calculations