4ZTE | pdb_00004zte

Crystal structure of human E-Cadherin (residues 3-213) in complex with a peptidomimetic inhibitor

• PDB DOI: https://doi.org/10.2210/pdb4ZTE/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-14 Released: 2016-06-01 
• Deposition Author(s): Nardone, V., Lucarelli, A.P., Dalle Vedove, A., Parisini, E.
• Funding Organization(s): European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Human E-Cadherin-EC1EC2 in Complex with a Peptidomimetic Competitive Inhibitor of Cadherin Homophilic Interaction.

Nardone, V., Lucarelli, A.P., Dalle Vedove, A., Fanelli, R., Tomassetti, A., Belvisi, L., Civera, M., Parisini, E.

(2016) J Med Chem 59: 5089-5094

• PubMed: 27120112 
• DOI: https://doi.org/10.1021/acs.jmedchem.5b01487
• Primary Citation of Related Structures:  
  4ZT1, 4ZTE


• PubMed Abstract: 
  

  Cadherins are transmembrane cell adhesion proteins whose aberrant expression often correlates with cancer development and proliferation. We report the crystal structure of an E-cadherin extracellular fragment in complex with a peptidomimetic compound that was previously shown to partially inhibit cadherin homophilic adhesion. The structure reveals an unexpected binding mode and allows the identification of a druggable cadherin interface, thus paving the way to a future structure-guided design of cell adhesion inhibitors against cadherin-expressing solid tumors.

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Organizational Affiliation: 

Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia , Via G. Pascoli 70/3, 20133 Milano, Italy.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47.09 kDa 
• Atom Count: 3,513 
• Modelled Residue Count: 420 
• Deposited Residue Count: 422 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cadherin-1	A, B	211	Homo sapiens	Mutation(s): 0  Gene Names: CDH1, CDHE, UVO
UniProt & NIH Common Fund Data Resources
Find proteins for P12830 (Homo sapiens) Explore P12830  Go to UniProtKB:  P12830
PHAROS:  P12830 GTEx:  ENSG00000039068

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4RL	F [auth A], J [auth B]	N-{[(2S,5S)-1-benzyl-5-(2-{[(2S,3S)-1-(tert-butylamino)-3-methyl-1-oxopentan-2-yl]amino}-2-oxoethyl)-3,6-dioxopiperazin-2-yl]methyl}-L-alpha-asparagine C28 H42 N6 O7 QOSIRQNYWJNZFB-WGLQCKHLSA-N
CA	C [auth A], D [auth A], E [auth A], G [auth B], H [auth B], I [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.13 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.579	α = 90
b = 76.835	β = 111.14
c = 72.772	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOLREP	phasing
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-06-01 
Deposition Author(s): Nardone, V., Lucarelli, A.P., Dalle Vedove, A., Parisini, E.

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Funding Organization	Location	Grant Number
European Union		FP7-PEOPLE-2010-RG (N. 268231)

Revision History  

• Version 1.0: 2016-06-01
  Type: Initial release
  
• Version 1.1: 2016-06-08
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description