5UWS

Crystal Structure of X11L2 NES Peptide in complex with CRM1-Ran-RanBP1

  • Classification: PROTEIN TRANSPORT
  • Organism(s): Homo sapiens, Saccharomyces cerevisiae
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): No 

  • Deposited: 2017-02-21 Released: 2017-03-22 
  • Deposition Author(s): Fung, H.Y.J., Chook, Y.M.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), Croucher Foundation, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Welch Foundation, Leukemia & Lymphoma Society, University of Texas Southwestern Medical Center, Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Nuclear export receptor CRM1 recognizes diverse conformations in nuclear export signals.

Fung, H.Y.Fu, S.C.Chook, Y.M.

(2017) Elife 6

  • DOI: 10.7554/eLife.23961
  • Primary Citation of Related Structures:  
    5UWP, 5UWO, 5UWR, 5UWQ, 5UWT, 5UWS, 5UWU, 5UWH, 5UWJ, 5UWI, 5UWW

  • PubMed Abstract: 
  • Nuclear export receptor CRM1 binds highly variable nuclear export signals (NESs) in hundreds of different cargoes. Previously we have shown that CRM1 binds NESs in both polypeptide orientations (Fung et al., 2015). Here, we show crystal structures of CRM1 bound to eight additional NESs which reveal diverse conformations that range from loop-like to all-helix, which occupy different extents of the invariant NES-binding groove ...

    Nuclear export receptor CRM1 binds highly variable nuclear export signals (NESs) in hundreds of different cargoes. Previously we have shown that CRM1 binds NESs in both polypeptide orientations (Fung et al., 2015). Here, we show crystal structures of CRM1 bound to eight additional NESs which reveal diverse conformations that range from loop-like to all-helix, which occupy different extents of the invariant NES-binding groove. Analysis of all NES structures show 5-6 distinct backbone conformations where the only conserved secondary structural element is one turn of helix that binds the central portion of the CRM1 groove. All NESs also participate in main chain hydrogen bonding with human CRM1 Lys568 side chain, which acts as a specificity filter that prevents binding of non-NES peptides. The large conformational range of NES backbones explains the lack of a fixed pattern for its 3-5 hydrophobic anchor residues, which in turn explains the large array of peptide sequences that can function as NESs.


    Organizational Affiliation

    Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GTP-binding nuclear protein RanA237Homo sapiensMutation(s): 0 
Gene Names: RANARA24OK/SW-cl.81
UniProt & NIH Common Fund Data Resources
Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
PHAROS:  P62826
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ran-specific GTPase-activating protein 1B143Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YRB1CST20HTN1SFO1YDR002WYD8119.08
UniProt
Find proteins for P41920 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P41920 
Go to UniProtKB:  P41920
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Exportin-1,Exportin-1C1024Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CRM1KAP124XPO1YGR218WG8514
UniProt
Find proteins for P30822 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P30822 
Go to UniProtKB:  P30822
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Amyloid beta A4 precursor protein-binding family A member 3D22Homo sapiensMutation(s): 0 
Gene Names: X11L2APBA3MINT3
UniProt & NIH Common Fund Data Resources
Find proteins for O96018 (Homo sapiens)
Explore O96018 
Go to UniProtKB:  O96018
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
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 A], 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: 0.222 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.646α = 90
b = 106.646β = 90
c = 304.628γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United StatesInternational Student Research Fellowship
Croucher FoundationHong KongPredoc Research Scholarship
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM069909
Welch FoundationUnited StatesI-1532
Leukemia & Lymphoma SocietyUnited StatesScholar Award
University of Texas Southwestern Medical CenterUnited StatesEndowed Scholars Program
Cancer Prevention and Research Institute of Texas (CPRIT)United StatesRP120352, RP150053

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-22
    Type: Initial release
  • Version 1.1: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-04-24
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-11-20
    Changes: Author supporting evidence