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- PDB-3lnh: Crystal structure of E-cadherin EC12 W2A -

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Basic information

Entry
Database: PDB / ID: 3lnh
TitleCrystal structure of E-cadherin EC12 W2A
ComponentsCadherin-1
KeywordsCELL ADHESION / cadherin / Calcium / 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 / desmosome assembly / salivary gland cavitation / regulation of branching involved in salivary gland morphogenesis / 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 / salivary gland cavitation / regulation of branching involved in salivary gland morphogenesis / Adherens junctions interactions / RHO GTPases activate IQGAPs / Degradation of the extracellular matrix / Integrin cell surface interactions / positive regulation of cell-cell adhesion / desmosome / lateral loop / regulation of protein localization to cell surface / alpha-catenin binding / trophectodermal cell differentiation / calcium-dependent cell-cell adhesion / bicellular tight junction assembly / flotillin complex / intestinal epithelial cell development / Schmidt-Lanterman incisure / cell-cell adhesion mediated by cadherin / catenin complex / epithelial cell morphogenesis / regulation of neuron migration / node of Ranvier / negative regulation of protein processing / apical junction complex / homophilic cell-cell adhesion / microvillus / decidualization / cochlea development / canonical Wnt signaling pathway / establishment of skin barrier / negative regulation of protein localization to plasma membrane / cytoskeletal protein binding / positive regulation of protein localization / axon terminus / embryo implantation / cell periphery / protein localization to plasma membrane / adherens junction / cellular response to amino acid stimulus / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / cell-cell adhesion / beta-catenin binding / negative regulation of epithelial cell proliferation / apical part of cell / cell-cell junction / regulation of protein localization / regulation of gene expression / actin cytoskeleton organization / 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: 2.6 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: 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_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)46,5328
Polymers46,2912
Non-polymers2406
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.536, 80.857, 72.519
Angle α, β, γ (deg.)90.00, 116.84, 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: 23145.734 Da / Num. of mol.: 2 / Fragment: UNP residues 157-369 / Mutation: W2A
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.: 157 / 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: 3.41 Å3/Da / Density % sol: 63.89 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 0.1M Tris, pH 8.5, 1.3M ammonium sulfate, 15% glycerol, 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
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: 2.6→50 Å / Num. obs: 19548 / % possible obs: 100 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 12.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0072refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EDH

1edh


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.877 / Cross valid method: THROUGHOUT / ESU R: 0.484 / ESU R Free: 0.299 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 998 5.1 %RANDOM
Rwork0.227 ---
obs0.229 18549 98.4 %-
all-18549 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.73 Å2
Baniso -1Baniso -2Baniso -3
1-1.96 Å20 Å23.23 Å2
2---0.17 Å20 Å2
3---1.13 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3196 0 6 157 3359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223254
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9951.9644436
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9125416
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87526.111144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81115538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1151512
X-RAY DIFFRACTIONr_chiral_restr0.2320.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212460
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4881.52088
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.91723414
X-RAY DIFFRACTIONr_scbond_it0.7931166
X-RAY DIFFRACTIONr_scangle_it1.5534.51022
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.57→2.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 55 -
Rwork0.294 1152 -
obs--82.11 %

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