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- PDB-4zt1: Crystal structure of human E-Cadherin (residues 3-213) in x-dimer... -

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Basic information

Entry
Database: PDB / ID: 4zt1
TitleCrystal structure of human E-Cadherin (residues 3-213) in x-dimer conformation
ComponentsCadherin-1
KeywordsCELL ADHESION / adhesion / cadherin / calcium-binding protein / x-dimer.
Function / homology
Function and homology information


response to Gram-positive bacterium / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cellular response to indole-3-methanol / flotillin complex / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Formation of definitive endoderm ...response to Gram-positive bacterium / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cellular response to indole-3-methanol / flotillin complex / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Formation of definitive endoderm / Adherens junctions interactions / catenin complex / Apoptotic cleavage of cell adhesion proteins / GTPase activating protein binding / cell-cell junction assembly / adherens junction organization / apical junction complex / ankyrin binding / negative regulation of cell-cell adhesion / cellular response to lithium ion / homophilic cell adhesion via plasma membrane adhesion molecules / lateral plasma membrane / RHO GTPases activate IQGAPs / Integrin cell surface interactions / cell adhesion molecule binding / synapse assembly / InlA-mediated entry of Listeria monocytogenes into host cells / Degradation of the extracellular matrix / negative regulation of cell migration / protein tyrosine kinase binding / protein localization to plasma membrane / adherens junction / cell morphogenesis / trans-Golgi network / cytoplasmic side of plasma membrane / response to toxic substance / beta-catenin binding / cell-cell adhesion / positive regulation of protein import into nucleus / neuron projection development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / actin cytoskeleton / lamellipodium / cell junction / postsynapse / regulation of gene expression / endosome / response to xenobiotic stimulus / cadherin binding / glutamatergic synapse / calcium ion binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherins / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsNardone, V. / Lucarelli, A.P. / Dalle Vedove, A. / Parisini, E.
Funding support1items
OrganizationGrant numberCountry
European UnionFP7-PEOPLE-2010-RG (N. 268231)
CitationJournal: J.Med.Chem. / Year: 2016
Title: Crystal Structure of Human E-Cadherin-EC1EC2 in Complex with a Peptidomimetic Competitive Inhibitor of Cadherin Homophilic Interaction.
Authors: Nardone, V. / Lucarelli, A.P. / Dalle Vedove, A. / Fanelli, R. / Tomassetti, A. / Belvisi, L. / Civera, M. / Parisini, E.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 1, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cadherin-1
B: Cadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9398
Polymers45,6992
Non-polymers2406
Water6,882382
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1820 Å2
ΔGint-32 kcal/mol
Surface area21920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.446, 76.417, 73.020
Angle α, β, γ (deg.)90.00, 109.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cadherin-1 / CAM 120/80 / Epithelial cadherin / E-cadherin / Uvomorulin


Mass: 22849.428 Da / Num. of mol.: 2 / Fragment: UNP residues 157-367
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDH1, CDHE, UVO / Plasmid: pET3a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P12830
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 382 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.46 Å3/Da / Density % sol: 64.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: TRIS 0.1 M, ammonium sulfate 1.3 M, calcium chloride 50 mM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.87→42.66 Å / Num. obs: 48085 / % possible obs: 86.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 8.4
Reflection shellResolution: 1.87→1.97 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 2.2 / % possible all: 58.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALAdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O72

2o72


Resolution: 1.92→42.65 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.066 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 2350 5 %RANDOM
Rwork0.19277 ---
obs0.1941 44649 98.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.422 Å2
Baniso -1Baniso -2Baniso -3
1-3.76 Å2-0 Å21.52 Å2
2---1.73 Å2-0 Å2
3----2.48 Å2
Refinement stepCycle: LAST / Resolution: 1.92→42.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 6 382 3568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.023238
X-RAY DIFFRACTIONr_bond_other_d0.0010.023028
X-RAY DIFFRACTIONr_angle_refined_deg0.5071.9574414
X-RAY DIFFRACTIONr_angle_other_deg0.45537016
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1525416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.08726.429140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7115526
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5861510
X-RAY DIFFRACTIONr_chiral_restr0.0430.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0213656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02646
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3094.2891670
X-RAY DIFFRACTIONr_mcbond_other5.3074.2861669
X-RAY DIFFRACTIONr_mcangle_it6.8366.4082084
X-RAY DIFFRACTIONr_mcangle_other6.8376.4122085
X-RAY DIFFRACTIONr_scbond_it6.7764.8921568
X-RAY DIFFRACTIONr_scbond_other6.7564.8791565
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.2667.0682329
X-RAY DIFFRACTIONr_long_range_B_refined14.12435.5313813
X-RAY DIFFRACTIONr_long_range_B_other11.17334.9443599
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 170 -
Rwork0.315 3236 -
obs--98.58 %

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