6X2P

Crystal Structure of the Mek1NES peptide bound to CRM1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

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Literature

Recognition of nuclear export signals by CRM1 carrying the oncogenic E571K mutation.

Baumhardt, J.M.Walker, J.S.Lee, Y.Shakya, B.Brautigam, C.A.Lapalombella, R.Grishin, N.Chook, Y.M.

(2020) Mol Biol Cell 31: 1879-1891

  • DOI: 10.1091/mbc.E20-04-0233
  • Primary Citation of Related Structures:  
    6X2M, 6X2O, 6X2P, 6X2R, 6X2S, 6X2U, 6X2V, 6X2W, 6X2X, 6X2Y

  • PubMed Abstract: 
  • The E571K mutation of CRM1 is highly prevalent in some cancers, but its mechanism of tumorigenesis is unclear. Glu571 of CRM1 is located in its nuclear export signal (NES)-binding groove, suggesting that binding of select NESs may be altered. We generated HEK 293 cells with either monoallelic CRM1WT/E571K or biallelic CRM1E571K/E571K using CRISPR/Cas9 ...

    The E571K mutation of CRM1 is highly prevalent in some cancers, but its mechanism of tumorigenesis is unclear. Glu571 of CRM1 is located in its nuclear export signal (NES)-binding groove, suggesting that binding of select NESs may be altered. We generated HEK 293 cells with either monoallelic CRM1WT/E571K or biallelic CRM1E571K/E571K using CRISPR/Cas9. We also combined analysis of binding affinities and structures of 27 diverse NESs for wild-type and E571K CRM1 with structure-based bioinformatics. While most NESs bind the two CRM1 similarly, NESs from Mek1, eIF4E-transporter, and RPS2 showed >10-fold affinity differences. These NESs have multiple charged side chains binding close to CRM1 position 571, but this feature alone was not sufficient to predict different binding to CRM1(E571K). Consistent with eIF4E-transporter NES binding weaker to CRM1(E571K), eIF4E-transporter was mislocalized in tumor cells carrying CRM1(E571K). This serves as proof of concept that understanding how CRM1(E571K) affects NES binding provides a platform for identifying cargoes that are mislocalized in cancer upon CRM1 mutation. Finally, we showed that large affinity changes seen with some NES peptides (of Mek1 and RPS2) do not always translate to the full-length cargoes, suggesting limitations with current NES prediction methods. Therefore, comprehensive studies like ours are imperative to identify CRM1 cargoes with real pathogenic potential.


    Organizational Affiliation

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding nuclear protein RanA216Homo sapiensMutation(s): 0 
Gene Names: RANARA24OK/SW-cl.81
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Find proteins for P62826 (Homo sapiens)
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PHAROS:  P62826
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UniProt GroupP62826
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ran-specific GTPase-activating protein 1B140Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YRB1CST20HTN1SFO1YDR002WYD8119.08
UniProt
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P41920
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UniProt GroupP41920
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exportin-1C1024Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CRM1KAP124XPO1YGR218WG8514
UniProt
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP30822
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Dual specificity mitogen-activated protein kinase kinase 1D17Homo sapiensMutation(s): 0 
Gene Names: MAP2K1MEK1PRKMK1
EC: 2.7.12.2
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Find proteins for Q02750 (Homo sapiens)
Explore Q02750 
Go to UniProtKB:  Q02750
PHAROS:  Q02750
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UniProt GroupQ02750
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
E [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth C],
I [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.924α = 90
b = 106.924β = 90
c = 303.928γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-05-20 
  • Released Date: 2020-07-01 
  • Deposition Author(s): Baumhardt, J.M.

Funding OrganizationLocationGrant Number
Cancer Prevention and Research Institute of Texas (CPRIT)--
Welch Foundation--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-08-12
    Changes: Database references