5UWR

Crystal Structure of CDC7 NES Peptide (extended) 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: 2.24 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


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
  • Structures With Same Primary Citation

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GTP-binding nuclear protein RanA237Homo sapiensMutation(s): 0 
Gene Names: RANARA24OK/SW-cl.81
Find proteins for P62826 (Homo sapiens)
Explore P62826 
Go to UniProtKB:  P62826
NIH Common Fund Data Resources
PHAROS  P62826
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Exportin-1C1024Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CRM1KAP124XPO1YGR218WG8514
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 LengthOrganismDetails
Cell division cycle 7-related protein kinaseD27Homo sapiensMutation(s): 0 
Gene Names: CDC7CDC7L1
EC: 2.7.11.1
Find proteins for O00311 (Homo sapiens)
Explore O00311 
Go to UniProtKB:  O00311
NIH Common Fund Data Resources
PHAROS  O00311
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ran-specific GTPase-activating protein 1B143Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: YRB1CST20HTN1SFO1YDR002WYD8119.08
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
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download CCD File 
A
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
C
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.085α = 90
b = 106.085β = 90
c = 304.551γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data collection
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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 

  • 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