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- PDB-1edh: E-CADHERIN DOMAINS 1 AND 2 IN COMPLEX WITH CALCIUM -

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Basic information

Entry
Database: PDB / ID: 1edh
TitleE-CADHERIN DOMAINS 1 AND 2 IN COMPLEX WITH CALCIUM
ComponentsE-CADHERINCadherin-1
KeywordsCELL ADHESION PROTEIN / CADHERIN / CALCIUM BINDING PROTEIN
Function / homology
Function and homology information


uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / salivary gland cavitation / regulation of branching involved in salivary gland morphogenesis / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / RHO GTPases activate IQGAPs / Adherens junctions interactions / Degradation of the extracellular matrix / Integrin cell surface interactions / regulation of neuron migration ...uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / salivary gland cavitation / regulation of branching involved in salivary gland morphogenesis / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / RHO GTPases activate IQGAPs / Adherens junctions interactions / Degradation of the extracellular matrix / Integrin cell surface interactions / regulation of neuron migration / positive regulation of cell-cell adhesion / lateral loop / cell-cell adhesion mediated by cadherin / negative regulation of axon extension / regulation of protein localization to cell surface / trophectodermal cell differentiation / alpha-catenin binding / flotillin complex / epithelial cell morphogenesis / Schmidt-Lanterman incisure / bicellular tight junction assembly / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / intestinal epithelial cell development / node of Ranvier / protein metabolic process / catenin complex / negative regulation of protein processing / cell-cell junction assembly / negative regulation of protein localization to plasma membrane / adherens junction organization / apical junction complex / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / microvillus / decidualization / canonical Wnt signaling pathway / establishment of skin barrier / axon terminus / synapse assembly / cytoskeletal protein binding / embryo implantation / protein tyrosine kinase binding / protein localization to plasma membrane / cell periphery / sensory perception of sound / cellular response to amino acid stimulus / adherens junction / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / beta-catenin binding / cell-cell adhesion / regulation of protein localization / negative regulation of epithelial cell proliferation / cell-cell junction / apical part of cell / actin cytoskeleton organization / postsynapse / regulation of gene expression / basolateral plasma membrane / protein phosphatase binding / in utero embryonic development / molecular adaptor activity / endosome / cadherin binding / protein domain specific binding / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / cell surface / identical protein binding / plasma membrane / cytoplasm
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 speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / THE INITIAL MODEL WAS OBTAINED FROM A COMBINATION OF MULTI-WAVELENGTH ANOMALOUS DIFFRACTION (MAD), REAL SPACE AVERAGING TECHNIQUES. THE MAD DATA WAS TAKEN AT THE MERCURY L(III) EDGE AT 3 DIFFERENT WAVELENGTHS (CHESS BEAMLINE F2). REAL SPACE AVERAGING WAS USED TO IMPROVE THE MAPS. / Resolution: 2 Å
AuthorsNagar, B. / Overduin, M. / Ikura, M. / Rini, J.M.
CitationJournal: Nature / Year: 1996
Title: Structural basis of calcium-induced E-cadherin rigidification and dimerization.
Authors: Nagar, B. / Overduin, M. / Ikura, M. / Rini, J.M.
History
DepositionMay 15, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E-CADHERIN
B: E-CADHERIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,07910
Polymers49,4372
Non-polymers6428
Water4,486249
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.657, 80.802, 72.635
Angle α, β, γ (deg.)90.00, 116.65, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHE ASYMMETRIC UNIT (MOLECULES A AND B) CONTAINS A CALCIUM MEDIATED DIMER. BOTH MOLECULES IN THE ASYMMETRIC UNIT CONTAIN THREE CALCIUM IONS (CA 2+) AND ONE MERCURY ATOM (HG). THE MERCURY ATOMS ARE BOUND TO AN EXPOSED CYSTEINE RESIDUE IN THE N-TERMINAL DOMAIN.

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Components

#1: Protein E-CADHERIN / Cadherin-1 / EPITHELIAL CADHERIN DOMAINS 1 AND 2 / ECAD12


Mass: 24718.504 Da / Num. of mol.: 2 / Mutation: INS(MR-D1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Tissue: EPITHELIAL / Cellular location: CELL SURFACECell membrane / Plasmid: PAS / Production host: Escherichia coli (E. coli) / Strain (production host): AR58 / References: UniProt: P09803
#2: Chemical ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Hg
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.23 Å3/Da / Density % sol: 62 %
Crystal growpH: 9
Details: 1.2 M AMMONIUM SULFATE 0.01 M CALCIUM CHLORIDE 0.1 M TRIS-HCL BUFFER, PH 9.0 0.003 M SODIUM AZIDE
Crystal grow
*PLUS
pH: 7.25 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
111 mg/mlprotein1drop
220 mMTris-HCl1drop
35 mMdithiothreitol1drop
40.05 mMsodium azide1drop
51.2 Mammonium sulfate1reservoir
65-10 mMcalcium chloride1reservoir
7100 mMTris-HCl1reservoir
83 mMsodium azide1reservoir

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.908
DetectorType: PRINCETON 2K / Detector: CCD / Date: Apr 3, 1995
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.908 Å / Relative weight: 1
ReflectionResolution: 2→22 Å / Num. obs: 37605 / % possible obs: 88.3 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Biso Wilson estimate: 26.08 Å2 / Rsym value: 0.053 / Net I/σ(I): 13
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.59 % / Rsym value: 0.146 / % possible all: 63.6
Reflection
*PLUS
Num. measured all: 86202 / Rmerge(I) obs: 0.053

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: THE INITIAL MODEL WAS OBTAINED FROM A COMBINATION OF MULTI-WAVELENGTH ANOMALOUS DIFFRACTION (MAD), REAL SPACE AVERAGING TECHNIQUES. THE MAD DATA WAS TAKEN AT THE ...Method to determine structure: THE INITIAL MODEL WAS OBTAINED FROM A COMBINATION OF MULTI-WAVELENGTH ANOMALOUS DIFFRACTION (MAD), REAL SPACE AVERAGING TECHNIQUES. THE MAD DATA WAS TAKEN AT THE MERCURY L(III) EDGE AT 3 DIFFERENT WAVELENGTHS (CHESS BEAMLINE F2). REAL SPACE AVERAGING WAS USED TO IMPROVE THE MAPS.
Resolution: 2→5 Å / Data cutoff high absF: 83.4 / σ(F): 2
Details: THE ELECTRON DENSITY FOR THE LOOP BETWEEN STRANDS B AND C (RESIDUES 27 - 32) IS WEAK.
RfactorNum. reflection% reflection
Rfree0.262 3333 10 %
Rwork0.206 --
obs0.206 33174 -
Displacement parametersBiso mean: 29.89 Å2
Refinement stepCycle: LAST / Resolution: 2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3228 0 8 249 3485
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.375
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.96
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.198
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2→2.07 Å
RfactorNum. reflection% reflection
Rfree0.256 209 9.6 %
Rwork0.257 1961 -
obs--54.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX_3.1.PROTOPHCSDX_3.1.PRO
X-RAY DIFFRACTION2CAD.PARNCAD.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.966
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.198

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