6E4L | pdb_00006e4l

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

• PDB DOI: https://doi.org/10.2210/pdb6E4L/pdb

• Classification: ENDOCYTOSIS
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-07-17 Released: 2019-04-24 
• Deposition Author(s): Dejonghe, W., Sharma, I., Denoo, B., Munck, S.D., Bulut, H., Mylle, E., Vasileva, M., Lu, Q., Savatin, D.V., Mishev, K., Nerinckx, W., Staes, A., Drozdzecki, A., Audenaert, D., Madder, A., Friml, J., Damme, D.V., Gevaert, K., Haucke, V., Savvides, S., Winne, J., Russinova, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.214 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

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

• PubMed: 31011214 
• DOI: https://doi.org/10.1038/s41589-019-0262-1
• Primary Citation Related Structures: 
  6E4L


• 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 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.

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Organizational Affiliation: 
• Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
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.
Department of Organic and Macromolecular Chemistry, Ghent University, Ghent, Belgium.
Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
Unit for Structural Biology, Center for Inflammation Research, VIB, Ghent, Belgium.
Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria.
Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany.
Ghent University Expertise Centre for Transmission Electron Microscopy and VIB BioImaging Core, Ghent, Belgium.
Institute of Science and Technology, Klosterneuburg, Austria.
Center for Medical Biotechnology, VIB, Ghent, Belgium.
Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
VIB Screening Core, Ghent, Belgium.
Expertise Centre for Bioassay Development and Screening, Ghent University, Ghent, Belgium.
Department of Molecular Pharmacology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology, Berlin, Germany.
Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. [e-mail].
Center for Plant Systems Biology, VIB, Ghent, Belgium. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.97 kDa 
• Atom Count: 3,068 
• Modeled Residue Count: 358 
• Deposited Residue Count: 369 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Clathrin heavy chain 1	A	369	Homo sapiens	Mutation(s): 0  Gene Names: CLTC, CLH17, CLTCL2, KIAA0034
UniProt & NIH Common Fund Data Resources
Find proteins for Q00610 (Homo sapiens) Explore Q00610  Go to UniProtKB:  Q00610
PHAROS:  Q00610 GTEx:  ENSG00000141367

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HRS	J [auth A]	5-bromo-N-(4-nitrophenyl)thiophene-2-sulfonamide C10 H7 Br N2 O4 S2 XAKPASIXPSBWRB-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	B [auth A], C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	G [auth A], H [auth A], I [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.214 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.21	α = 90
b = 74.34	β = 90
c = 84.23	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-24 
Deposition Author(s): Dejonghe, W., Sharma, I., Denoo, B., Munck, S.D., Bulut, H., Mylle, E., Vasileva, M., Lu, Q., Savatin, D.V., Mishev, K., Nerinckx, W., Staes, A., Drozdzecki, A., Audenaert, D., Madder, A., Friml, J., Damme, D.V., Gevaert, K., Haucke, V., Savvides, S., Winne, J., Russinova, E.

Revision History  

• Version 1.0: 2019-04-24
  Type: Initial release
  
• Version 1.1: 2019-05-08
  Changes: Data collection, Database references
• Version 1.2: 2019-05-29
  Changes: Data collection, Database references
• Version 1.3: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description