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 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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: 10.1016/j.celrep.2015.09.042

  • 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 tig ...

    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.


    Related Citations: 
    • Combining dehydration, construct optimization and improved data collection to solve the crystal structure of a CRM1-RanGTP-SPN1-Nup214 quaternary export complex
      Monecke, T.,Dickmanns, A.,Weiss, M.S.,Port, S.A.,Kehlenbach, R.H.,Ficner, R.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exportin-1
A
1044Homo sapiensMutation(s): 0 
Gene Names: XPO1 (CRM1)
Find proteins for O14980 (Homo sapiens)
Go to Gene View: XPO1
Go to UniProtKB:  O14980
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GTP-binding nuclear protein Ran
B
172Homo sapiensMutation(s): 1 
Gene Names: RAN (ARA24)
Find proteins for P62826 (Homo sapiens)
Go to Gene View: RAN
Go to UniProtKB:  P62826
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Snurportin-1
C
289Homo sapiensMutation(s): 0 
Gene Names: SNUPN (RNUT1, SPN1)
Find proteins for O95149 (Homo sapiens)
Go to Gene View: SNUPN
Go to UniProtKB:  O95149
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Maltose-binding periplasmic protein,Nuclear pore complex protein Nup214
D
479Escherichia coli (strain K12)Homo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malE, NUP214 (CAIN, CAN, KIAA0023)
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AEX9
Find proteins for P35658 (Homo sapiens)
Go to Gene View: NUP214
Go to UniProtKB:  P35658
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAL
Query on MAL

Download SDF File 
Download CCD File 
A
MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
 Ligand Interaction
GTP
Query on GTP

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Download CCD File 
B
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PRO
Query on PRO

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Download CCD File 
A, C
PROLINE
C5 H9 N O2
ONIBWKKTOPOVIA-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.206 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 112.330α = 90.00
b = 248.970β = 90.00
c = 210.570γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XSCALEdata scaling
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
DFGGermanySFB860

Revision History 

  • Version 1.0: 2015-11-04
    Type: Initial release