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- PDB-3lne: Crystal structure of E-cadherin EC12 K14E -

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Basic information

Entry
Database: PDB / ID: 3lne
TitleCrystal structure of E-cadherin EC12 K14E
ComponentsCadherin-1
KeywordsCELL ADHESION / cadherin / Calcium / Cell junction / Cell membrane / Glycoprotein / Transmembrane
Function / homology
Function and homology information


uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / desmosome assembly / regulation of branching involved in salivary gland morphogenesis / salivary gland cavitation / Adherens junctions interactions / RHO GTPases activate IQGAPs / Degradation of the extracellular matrix / Integrin cell surface interactions / positive regulation of cell-cell adhesion ...uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / desmosome assembly / regulation of branching involved in salivary gland morphogenesis / salivary gland cavitation / Adherens junctions interactions / RHO GTPases activate IQGAPs / Degradation of the extracellular matrix / Integrin cell surface interactions / positive regulation of cell-cell adhesion / lateral loop / desmosome / regulation of protein localization to cell surface / regulation of neuron migration / epithelial cell morphogenesis / alpha-catenin binding / trophectodermal cell differentiation / bicellular tight junction assembly / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Schmidt-Lanterman incisure / flotillin complex / intestinal epithelial cell development / cell-cell adhesion mediated by cadherin / catenin complex / node of Ranvier / negative regulation of protein processing / apical junction complex / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / microvillus / decidualization / establishment of skin barrier / canonical Wnt signaling pathway / negative regulation of protein localization to plasma membrane / cytoskeletal protein binding / positive regulation of protein localization / axon terminus / embryo implantation / protein localization to plasma membrane / cell periphery / adherens junction / cellular response to amino acid stimulus / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / beta-catenin binding / cell-cell adhesion / negative regulation of epithelial cell proliferation / apical part of cell / cell-cell junction / regulation of protein localization / actin cytoskeleton organization / regulation of gene expression / protein phosphatase binding / basolateral plasma membrane / molecular adaptor activity / in utero embryonic development / endosome / protein domain specific binding / axon / calcium ion binding / cell surface / Golgi apparatus / 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 / Cadherin / Catenin binding domain superfamily / Cadherins / Cadherin conserved site / Cadherin domain signature. ...Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Cadherin / Catenin binding domain superfamily / Cadherins / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / Cadherin-like superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJin, X. / Harrison, O. / Shapiro, L.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2010
Title: Two-step adhesive binding by classical cadherins.
Authors: Harrison, O.J. / Bahna, F. / Katsamba, P.S. / Jin, X. / Brasch, J. / Vendome, J. / Ahlsen, G. / Carroll, K.J. / Price, S.R. / Honig, B. / Shapiro, L.
History
DepositionFeb 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4735
Polymers23,2611
Non-polymers2124
Water5,441302
1
A: Cadherin-1
hetero molecules

A: Cadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,94610
Polymers46,5222
Non-polymers4258
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2250 Å2
ΔGint-43 kcal/mol
Surface area23150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.001, 48.536, 54.486
Angle α, β, γ (deg.)90.00, 111.63, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cadherin-1 / Epithelial cadherin / E-cadherin / Uvomorulin / ARC-1 / E-Cad/CTF1 / E-Cad/CTF2 / E-Cad/CTF3


Mass: 23260.801 Da / Num. of mol.: 1 / Fragment: UNP residues 157-369 / Mutation: K14E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh1 / Production host: Escherichia coli (E. coli) / References: UniProt: P09803
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 3.43 Å3/Da / Density % sol: 64.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 0.75M sodium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97897 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 16, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 21629 / Num. obs: 19964 / % possible obs: 92.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 23.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EDH

1edh


Resolution: 2→20 Å / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.2194 1022 5.16 %
Rwork0.1719 --
obs0.1744 19809 91.5 %
all-19964 -
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 9 302 1950

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