Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45939.32 
• Atom Count: 3186 
• Residue Count: 422 
• Unique protein chains: 1

4ZT1

Crystal structure of human E-Cadherin (residues 3-213) in x-dimer conformation

• DOI: 10.2210/pdb4ZT1/pdb

• Classification: CELL ADHESION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• 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: 1.92 Å
• R-Value Free: 0.219 
• R-Value Work: 0.193 

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: 10.1021/acs.jmedchem.5b01487
• Primary Citation of Related Structures:  
  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: 

Dipartimento di Chimica, Università degli Studi di Milano , Via C. Golgi 19, 20133 Milano, Italy.,Dipartimento di Scienza e Alta Tecnologia, Università degli Studi dell'Insubria , Via Valleggio 11, 22100 Como, Italy.,Dipartimento di Chimica, Materiali and Ingegneria Chimica "Giulio Natta", Politecnico di Milano , Via L. Mancinelli 7, 20131 Milano, Italy.,Center for Nano Science and Technology @PoliMi, Istituto Italiano di Tecnologia , Via G. Pascoli 70/3, 20133 Milano, Italy.,Dipartimento di Oncologia Sperimentale e Medicina Molecolare, Fondazione IRCCS Istituto Nazionale dei Tumori , Via G. Amadeo 42, 20133 Milano, Italy.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Cadherin-1	A, B	211	Homo sapiens	Mutation(s): 0  Gene Names: CDH1 (CDHE, UVO)
Find proteins for P12830 (Homo sapiens) Go to Gene View: CDH1 Go to UniProtKB:  P12830

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.92 Å
• R-Value Free: 0.219 
• R-Value Work: 0.193 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 120.446	α = 90.00
b = 76.417	β = 109.98
c = 73.020	γ = 90.00

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-05-14 
• 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
  Type: Database references