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- PDB-3l6x: Crystal structure of p120 catenin in complex with E-cadherin -

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Basic information

Entry
Database: PDB / ID: 3l6x
TitleCrystal structure of p120 catenin in complex with E-cadherin
Components
  • Catenin delta-1
  • E-cadherin
KeywordsCELL ADHESION / p120 / catenin / cadherin / E-cadherin / armadillo / ARM / JMD / complex / cell-cell adhesion / ARVCF / delta-catenin / p0071 / Dp120 / JAC-1 / Cell membrane / Membrane / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Wnt signaling pathway
Function / homology
Function and homology information


CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / response to Gram-positive bacterium / Regulation of CDH11 function / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / zonula adherens / negative regulation of axon extension / cell-cell adhesion mediated by cadherin ...CDH11 homotypic and heterotypic interactions / Regulation of CDH19 Expression and Function / response to Gram-positive bacterium / Regulation of CDH11 function / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / pituitary gland development / gamma-catenin binding / zonula adherens / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / cellular response to indole-3-methanol / presynaptic active zone cytoplasmic component / 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 / regulation of postsynaptic membrane neurotransmitter receptor levels / homophilic cell adhesion via plasma membrane adhesion molecules / lateral plasma membrane / RHO GTPases activate IQGAPs / postsynaptic density, intracellular component / Integrin cell surface interactions / cell adhesion molecule binding / synapse assembly / protein sequestering activity / InlA-mediated entry of Listeria monocytogenes into host cells / Degradation of the extracellular matrix / hippocampal mossy fiber to CA3 synapse / negative regulation of cell migration / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / protein localization to plasma membrane / adherens junction / Schaffer collateral - CA1 synapse / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / trans-Golgi network / cytoplasmic side of plasma membrane / response to toxic substance / beta-catenin binding / Wnt signaling pathway / cell-cell adhesion / positive regulation of protein import into nucleus / neuron projection development / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / cell-cell junction / actin cytoskeleton / lamellipodium / cell junction / midbody / growth cone / postsynapse / regulation of gene expression / dendritic spine / protein stabilization / endosome / response to xenobiotic stimulus / cadherin binding / signaling receptor binding / glutamatergic synapse / calcium ion binding / positive regulation of DNA-templated transcription / perinuclear region of cytoplasm / cell surface / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Plakophilin/Delta catenin / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / Cadherin conserved site / Cadherin domain signature. ...Plakophilin/Delta catenin / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily / Cadherin / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherins domain profile. / Cadherin-like / Cadherin-like superfamily / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Catenin delta-1 / Cadherin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsIshiyama, N. / Lee, S.-H. / Liu, S. / Li, G.-Y. / Smith, M.J. / Reichardt, L.F. / Ikura, M.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2010
Title: Dynamic and static interactions between p120 catenin and E-cadherin regulate the stability of cell-cell adhesion.
Authors: Ishiyama, N. / Lee, S.H. / Liu, S. / Li, G.Y. / Smith, M.J. / Reichardt, L.F. / Ikura, M.
History
DepositionDec 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 2023Group: 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 / 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 / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Catenin delta-1
B: E-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7546
Polymers67,3702
Non-polymers3844
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3050 Å2
ΔGint-64 kcal/mol
Surface area19970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.403, 92.403, 171.890
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Catenin delta-1 / p120 catenin / p120(ctn) / Cadherin-associated Src substrate / CAS / p120(cas)


Mass: 65348.980 Da / Num. of mol.: 1 / Fragment: p120 catenin isoform 4A / Mutation: deletion, residues 613-643
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTNND1, KIAA0384 / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O60716
#2: Protein/peptide E-cadherin


Mass: 2020.949 Da / Num. of mol.: 1 / Fragment: E-cadherin juxtamembrane domain core region / Source method: obtained synthetically / References: UniProt: P12830*PLUS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE OF THIS ENTRY MATCHES THE SEQUENCE OF ISOFORM 1A WITH UNIPROT IDENTIFIER O60716-5. ...THE SEQUENCE OF THIS ENTRY MATCHES THE SEQUENCE OF ISOFORM 1A WITH UNIPROT IDENTIFIER O60716-5. RESIDUES 626-631 (EXON C) OF O60716 ARE NOT PART OF ISOFORM 1A.

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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: 3.14 Å3/Da / Density % sol: 60.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Bis-Tris, 1.8 M Ammonium sulfate, 3% methanol, pH 5.6, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 24, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→35 Å / Num. obs: 33911 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rsym value: 0.057 / Χ2: 1.064 / Net I/σ(I): 10.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 7.088 / Num. unique all: 1674 / Rsym value: 0.394 / Χ2: 1.143 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.25 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å46.16 Å
Translation2.7 Å46.16 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.3phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-3000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XM9

1xm9


Resolution: 2.4→32 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.199 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.836 / SU B: 10.904 / SU ML: 0.127 / SU R Cruickshank DPI: 0.224 / SU Rfree: 0.193 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.226 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1707 5.1 %RANDOM
Rwork0.201 ---
obs0.203 33751 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.26 Å2 / Biso mean: 39.304 Å2 / Biso min: 17.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.21 Å20.6 Å20 Å2
2--1.21 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 2.4→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3503 0 20 117 3640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223603
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9664887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1225453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20524.643168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44915632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1021527
X-RAY DIFFRACTIONr_chiral_restr0.0860.2557
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212698
X-RAY DIFFRACTIONr_mcbond_it0.6441.52258
X-RAY DIFFRACTIONr_mcangle_it1.24623622
X-RAY DIFFRACTIONr_scbond_it2.14831345
X-RAY DIFFRACTIONr_scangle_it3.64.51263
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 141 -
Rwork0.242 2285 -
all-2426 -
obs--99.43 %
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)
11.48840.14331.43421.09810.69943.39520.0478-0.0302-0.0490.25360.1824-0.13430.37330.2466-0.23010.00650.0742-0.0749-0.1578-0.0467-0.134-35.3417.51533.924
21.53860.14480.02892.33210.50963.51810.03750.14340.0345-0.08180.04990.08010.0165-0.0782-0.0873-0.0604-0.0085-0.0473-0.14410.0321-0.1115-49.06511.57912.781
33.60591.1805-1.24991.2678-0.75191.4182-0.01780.56640.2629-0.0470.18920.0361-0.1414-0.1321-0.1715-0.0188-0.0428-0.0337-0.00550.0867-0.0277-41.48325.222-8.611
40.58460.37312.27510.66070.709810.3466-0.0130.06280.04990.002-0.0079-0.02080.06510.13070.02080.00510.023-0.0421-0.0039-0.0586-0.0149-32.48115.96739.143
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A358 - 509
2X-RAY DIFFRACTION2A520 - 599
3X-RAY DIFFRACTION3A645 - 846
4X-RAY DIFFRACTION4B758 - 775

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