6E4L

The structure of the N-terminal domain of human clathrin heavy chain 1 (nTD) in complex with ES9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Disruption of endocytosis through chemical inhibition of clathrin heavy chain function.

Dejonghe, W.Sharma, I.Denoo, B.De Munck, S.Lu, Q.Mishev, K.Bulut, H.Mylle, E.De Rycke, R.Vasileva, M.Savatin, D.V.Nerinckx, W.Staes, A.Drozdzecki, A.Audenaert, D.Yperman, K.Madder, A.Friml, J.Van Damme, D.Gevaert, K.Haucke, V.Savvides, S.N.Winne, J.Russinova, E.

(2019) Nat.Chem.Biol. 15: 641-649

  • DOI: 10.1038/s41589-019-0262-1

  • PubMed Abstract: 
  • Clathrin-mediated endocytosis (CME) is a highly conserved and essential cellular process in eukaryotic cells, but its dynamic and vital nature makes it challenging to study using classical genetics tools. In contrast, although small molecules can acu ...

    Clathrin-mediated endocytosis (CME) is a highly conserved and essential cellular process in eukaryotic cells, but its dynamic and vital nature makes it challenging to study using classical genetics tools. In contrast, although small molecules can acutely and reversibly perturb CME, the few chemical CME inhibitors that have been applied to plants are either ineffective or show undesirable side effects. Here, we identify the previously described endosidin9 (ES9) as an inhibitor of clathrin heavy chain (CHC) function in both Arabidopsis and human cells through affinity-based target isolation, in vitro binding studies and X-ray crystallography. Moreover, we present a chemically improved ES9 analog, ES9-17, which lacks the undesirable side effects of ES9 while retaining the ability to target CHC. ES9 and ES9-17 have expanded the chemical toolbox used to probe CHC function, and present chemical scaffolds for further design of more specific and potent CHC inhibitors across different systems.


    Organizational Affiliation

    Unit for Structural Biology, Center for Inflammation Research, VIB, Ghent, Belgium.,VIB Screening Core, Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,Expertise Centre for Bioassay Development and Screening, Ghent University, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,Center for Medical Biotechnology, VIB, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium. eurus@psb.vib-ugent.be.,Institute of Science and Technology, Klosterneuburg, Austria.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium.,Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria.,Department of Biology, Chemistry and Pharmacy, Freie Universit├Ąt Berlin, Berlin, Germany.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. eurus@psb.vib-ugent.be.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, USA.,Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,Ghent University Expertise Centre for Transmission Electron Microscopy and VIB BioImaging Core, Ghent, Belgium.,Department of Molecular Pharmacology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology, Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Clathrin heavy chain 1
A
369Homo sapiensMutation(s): 0 
Gene Names: CLTC (CLH17, CLTCL2, KIAA0034)
Find proteins for Q00610 (Homo sapiens)
Go to Gene View: CLTC
Go to UniProtKB:  Q00610
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
HRS
Query on HRS

Download SDF File 
Download CCD File 
A
5-bromo-N-(4-nitrophenyl)thiophene-2-sulfonamide
C10 H7 Br N2 O4 S2
XAKPASIXPSBWRB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.210α = 90.00
b = 74.340β = 90.00
c = 84.230γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-08
    Type: Data collection, Database references
  • Version 1.2: 2019-05-29
    Type: Data collection, Database references