5DIS

Crystal structure of a CRM1-RanGTP-SPN1 export complex bound to a 113 amino acid FG-repeat containing fragment of Nup214


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

Starting Models: experimental
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Literature

Structural and Functional Characterization of CRM1-Nup214 Interactions Reveals Multiple FG-Binding Sites Involved in Nuclear Export.

Port, S.A.Monecke, T.Dickmanns, A.Spillner, C.Hofele, R.Urlaub, H.Ficner, R.Kehlenbach, R.H.

(2015) Cell Rep 13: 690-702

  • DOI: https://doi.org/10.1016/j.celrep.2015.09.042
  • Primary Citation of Related Structures:  
    5DIS

  • PubMed Abstract: 

    CRM1 is the major nuclear export receptor. During translocation through the nuclear pore, transport complexes transiently interact with phenylalanine-glycine (FG) repeats of multiple nucleoporins. On the cytoplasmic side of the nuclear pore, CRM1 tightly interacts with the nucleoporin Nup214. Here, we present the crystal structure of a 117-amino-acid FG-repeat-containing fragment of Nup214, in complex with CRM1, Snurportin 1, and RanGTP at 2.85 Å resolution. The structure reveals eight binding sites for Nup214 FG motifs on CRM1, with intervening stretches that are loosely attached to the transport receptor. Nup214 binds to N- and C-terminal regions of CRM1, thereby clamping CRM1 in a closed conformation and stabilizing the export complex. The role of conserved hydrophobic pockets for the recognition of FG motifs was analyzed in biochemical and cell-based assays. Comparative studies with RanBP3 and Nup62 shed light on specificities of CRM1-nucleoporin binding, which serves as a paradigm for transport receptor-nucleoporin interactions.


  • Organizational Affiliation

    Department of Molecular Biology, Faculty of Medicine, GZMB, Georg-August-University Göttingen, Humboldtallee 23, 37073 Göttingen, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Exportin-11,044Homo sapiensMutation(s): 0 
Gene Names: XPO1CRM1
UniProt & NIH Common Fund Data Resources
Find proteins for O14980 (Homo sapiens)
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Go to UniProtKB:  O14980
GTEx:  ENSG00000082898 
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UniProt GroupO14980
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
GTP-binding nuclear protein Ran172Homo sapiensMutation(s): 1 
Gene Names: RANARA24OK/SW-cl.81
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Find proteins for P62826 (Homo sapiens)
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Go to UniProtKB:  P62826
GTEx:  ENSG00000132341 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Snurportin-1289Homo sapiensMutation(s): 0 
Gene Names: SNUPNRNUT1SPN1
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Find proteins for O95149 (Homo sapiens)
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Go to UniProtKB:  O95149
GTEx:  ENSG00000169371 
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UniProt GroupO95149
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose-binding periplasmic protein,Nuclear pore complex protein Nup214479Escherichia coli K-12Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malEb4034JW3994NUP214CAINCANKIAA0023
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Find proteins for P0AEX9 (Escherichia coli (strain K12))
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Go to UniProtKB:  P0AEX9
Find proteins for P35658 (Homo sapiens)
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Go to UniProtKB:  P35658
GTEx:  ENSG00000126883 
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UniProt GroupsP35658P0AEX9
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Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
E
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.33α = 90
b = 248.97β = 90
c = 210.57γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHASERphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB860

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Author supporting evidence, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-10
    Changes: Data collection, Database references, Refinement description, Structure summary