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- PDB-3lni: Crystal structure of E-cadherin EC12 E89A -

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Basic information

Entry
Database: PDB / ID: 3lni
TitleCrystal structure of E-cadherin EC12 E89A
ComponentsCadherin-1
KeywordsCELL ADHESION / cadherin / Cell junction / Cell membrane / Cleavage on pair of basic residues / Glycoprotein / Membrane / Transmembrane
Function / homology
Function and homology information


uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / regulation of branching involved in salivary gland morphogenesis / salivary gland cavitation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / Adherens junctions interactions / RHO GTPases activate IQGAPs / Degradation of the extracellular matrix / Integrin cell surface interactions / lateral loop ...uterine epithelium development / Apoptotic cleavage of cell adhesion proteins / regulation of branching involved in salivary gland morphogenesis / salivary gland cavitation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / Adherens junctions interactions / RHO GTPases activate IQGAPs / Degradation of the extracellular matrix / Integrin cell surface interactions / lateral loop / positive regulation of cell-cell adhesion / desmosome / protein metabolic process / negative regulation of axon extension / regulation of protein localization to cell surface / cell-cell adhesion mediated by cadherin / trophectodermal cell differentiation / regulation of neuron migration / epithelial cell morphogenesis / alpha-catenin binding / bicellular tight junction assembly / Schmidt-Lanterman incisure / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / flotillin complex / intestinal epithelial cell development / node of Ranvier / catenin complex / cell-cell junction assembly / adherens junction organization / negative regulation of protein processing / apical junction complex / cochlea development / homophilic cell adhesion via plasma membrane adhesion molecules / microvillus / decidualization / establishment of skin barrier / negative regulation of protein localization to plasma membrane / canonical Wnt signaling pathway / axon terminus / synapse assembly / cytoskeletal protein binding / embryo implantation / protein tyrosine kinase binding / 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 / cell morphogenesis / cell-cell adhesion / beta-catenin binding / negative regulation of epithelial cell proliferation / cell-cell junction / cell migration / apical part of cell / regulation of protein localization / actin cytoskeleton organization / regulation of gene expression / basolateral plasma membrane / protein phosphatase binding / in utero embryonic development / postsynapse / 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 / 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: 2.3 Å
AuthorsHarrison, O. / Jin, X. / 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: Advisory / 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 / pdbx_struct_special_symmetry / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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 / _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
B: Cadherin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6468
Polymers46,4062
Non-polymers2406
Water10,160564
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.630, 77.122, 71.675
Angle α, β, γ (deg.)90.00, 115.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-507-

HOH

21B-524-

HOH

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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: 23202.830 Da / Num. of mol.: 2 / Fragment: UNP residues 157-369 / Mutation: E89A
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.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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: 3.22 Å3/Da / Density % sol: 61.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.25M ammonium sulfate, 0.1M MES pH 6.5, 26% PEG 5000 monomethylether, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 17, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 28461 / Num. obs: 28177 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EDH

1edh


Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.919 / SU B: 10.341 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22753 1387 5 %RANDOM
Rwork0.16578 ---
all0.169 28177 --
obs0.1689 26309 98.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.417 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å22.45 Å2
2---0.19 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3194 0 6 564 3764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223263
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9624460
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5835418
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.18926140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33215529
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7731511
X-RAY DIFFRACTIONr_chiral_restr0.0890.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022471
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21355
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22207
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.2372
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0760.225
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6441.52147
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03723429
X-RAY DIFFRACTIONr_scbond_it1.831255
X-RAY DIFFRACTIONr_scangle_it2.9674.51029
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 103 -
Rwork0.208 1832 -
obs--94.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.07991.5647-5.97270.6252-1.93738.50550.49230.00170.72960.22440.10880.2159-0.5706-0.5052-0.6012-0.03880.05830.0565-0.1240.0423-0.12594.3789-1.562832.103
22.5596-1.6225-2.41391.70421.99354.9362-0.00830.11760.03360.02080.0238-0.032-0.0043-0.0617-0.0155-0.1906-0.0353-0.0091-0.2188-0.0032-0.195425.8338-11.3543-7.8796
36.5006-5.9112-1.80467.12632.18971.5774-0.3679-0.0935-0.44650.38070.1150.91410.0705-0.3660.2529-0.15460.08010.0215-0.10280.0835-0.02563.924218.087518.7076
49.6701-3.64640.13682.1787-0.26570.66510.20940.58920.4339-0.1989-0.2958-0.40380.10980.21740.0864-0.1450.08850.0161-0.1080.0678-0.090246.03211.273113.8603
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 102
2X-RAY DIFFRACTION2A103 - 213
3X-RAY DIFFRACTION3B1 - 102
4X-RAY DIFFRACTION4B103 - 213

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