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- PDB-3ifq: Interction of plakoglobin and beta-catenin with desmosomal cadherins -

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Basic information

Entry
Database: PDB / ID: 3ifq
TitleInterction of plakoglobin and beta-catenin with desmosomal cadherins
Components
  • E-cadherin
  • plakoglobin
KeywordsCELL ADHESION / armadillo repeat / Acetylation / Cardiomyopathy / Cell junction / Cytoplasm / Cytoskeleton / Disease mutation / Membrane / Palmoplantar keratoderma / Phosphoprotein / Polymorphism / Calcium / Cell membrane / Cleavage on pair of basic residues / Disulfide bond / Glycoprotein / Transmembrane
Function / homology
Function and homology information


gamma-catenin-TCF7L2 complex / endothelial cell-cell adhesion / nuclear receptor binding => GO:0016922 / cornification / desmosome assembly / uterine epithelium development / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / Apoptotic cleavage of cell adhesion proteins / Keratinization ...gamma-catenin-TCF7L2 complex / endothelial cell-cell adhesion / nuclear receptor binding => GO:0016922 / cornification / desmosome assembly / uterine epithelium development / bundle of His cell-Purkinje myocyte adhesion involved in cell communication / cell adhesive protein binding involved in bundle of His cell-Purkinje myocyte communication / Apoptotic cleavage of cell adhesion proteins / Keratinization / cytoskeletal protein-membrane anchor activity / regulation of branching involved in salivary gland morphogenesis / salivary gland cavitation / neutrophil degranulation / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / RHO GTPases activate IQGAPs / Adherens junctions interactions / desmosome / Degradation of the extracellular matrix / positive regulation of cell-cell adhesion / Integrin cell surface interactions / zonula adherens / lateral loop / regulation of neuron migration / detection of mechanical stimulus / negative regulation of axon extension / cell-cell adhesion mediated by cadherin / regulation of protein localization to cell surface / cellular response to indole-3-methanol / trophectodermal cell differentiation / alpha-catenin binding / Formation of the cornified envelope / epithelial cell morphogenesis / flotillin complex / Schmidt-Lanterman incisure / fascia adherens / bicellular tight junction assembly / apicolateral plasma membrane / cornified envelope / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / intestinal epithelial cell development / node of Ranvier / regulation of ventricular cardiac muscle cell action potential / protein metabolic process / Adherens junctions interactions / catenin complex / negative regulation of protein processing / cell-cell junction assembly / negative regulation of protein localization to plasma membrane / adherens junction organization / positive regulation of cell-matrix adhesion / apical junction complex / intermediate filament / cochlea development / keratinization / regulation of heart rate by cardiac conduction / homophilic cell adhesion via plasma membrane adhesion molecules / microvillus / negative regulation of blood vessel endothelial cell migration / decidualization / intercalated disc / lateral plasma membrane / canonical Wnt signaling pathway / establishment of skin barrier / axon terminus / cell adhesion molecule binding / synapse assembly / cytoskeletal protein binding / embryo implantation / protein tyrosine kinase binding / VEGFR2 mediated vascular permeability / cell periphery / protein localization to plasma membrane / protein-DNA complex / adherens junction / sensory perception of sound / cellular response to amino acid stimulus / negative regulation of canonical Wnt signaling pathway / cell morphogenesis / cytoplasmic side of plasma membrane / beta-catenin binding / positive regulation of DNA-binding transcription factor activity / Z disc / cell-cell adhesion / positive regulation of protein import into nucleus / specific granule lumen / positive regulation of angiogenesis / negative regulation of epithelial cell proliferation / regulation of protein localization / cell-cell junction / cell migration / actin cytoskeleton / positive regulation of canonical Wnt signaling pathway / apical part of cell / regulation of cell population proliferation / actin cytoskeleton organization / postsynapse / regulation of gene expression / basolateral plasma membrane / protein phosphatase binding
Similarity search - Function
Junction plakoglobin / TCF3-CBD (Catenin binding domain) / TCF3-CBD (Catenin binding domain) / Beta-catenin / Cadherin prodomain like / Cadherin prodomain / Cadherin prodomain like / Cadherin, Y-type LIR-motif / Cadherin, Y-type LIR-motif / Catenin binding domain superfamily ...Junction plakoglobin / TCF3-CBD (Catenin binding domain) / TCF3-CBD (Catenin binding domain) / Beta-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 / Few Secondary Structures / Irregular / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Mainly Alpha
Similarity search - Domain/homology
Cadherin-1 / Junction plakoglobin
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChoi, H.-J. / Gross, J.C. / Pokutta, S. / Weis, W.I.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Interactions of plakoglobin and beta-catenin with desmosomal cadherins: basis of selective exclusion of alpha- and beta-catenin from desmosomes.
Authors: Choi, H.J. / Gross, J.C. / Pokutta, S. / Weis, W.I.
History
DepositionJul 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: plakoglobin
B: plakoglobin
C: E-cadherin
D: E-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,5557
Polymers145,2674
Non-polymers2883
Water00
1
A: plakoglobin
C: E-cadherin
hetero molecules

B: plakoglobin
D: E-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,5557
Polymers145,2674
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area17270 Å2
ΔGint-76 kcal/mol
Surface area51040 Å2
MethodPISA
2
A: plakoglobin
C: E-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8254
Polymers72,6332
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-32 kcal/mol
Surface area27980 Å2
MethodPISA
3
B: plakoglobin
D: E-cadherin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,7293
Polymers72,6332
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6490 Å2
ΔGint-33 kcal/mol
Surface area27300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.043, 76.150, 122.940
Angle α, β, γ (deg.)90.00, 97.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein plakoglobin / Desmoplakin-3 / Desmoplakin III / Catenin gamma


Mass: 60574.820 Da / Num. of mol.: 2 / Fragment: residues 124-676
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JUP, CTNNG, DP3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P14923
#2: Protein E-cadherin / Epithelial cadherin / Cadherin-1 / Uvomorulin / ARC-1 / E-Cad/CTF1 / E-Cad/CTF2 / E-Cad/CTF3


Mass: 12058.477 Da / Num. of mol.: 2 / Fragment: residues 778-884
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cdh1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P09803
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4

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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: 2.43 Å3/Da / Density % sol: 49.41 %
Crystal growTemperature: 289.5 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 17% PEG 3350, 0.1M Ammonium sulfate, 0.1M Tris-Cl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289.5K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 17, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 34257 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 83.9 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 13.89
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I7W

1i7w


Resolution: 2.8→44.786 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 30.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2609 3424 10.01 %
Rwork0.1935 --
obs0.2005 34192 98.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.813 Å2 / ksol: 0.33 e/Å3
Displacement parametersBiso mean: 93.082 Å2
Baniso -1Baniso -2Baniso -3
1--15.3564 Å20 Å23.8841 Å2
2--4.4335 Å20 Å2
3---10.9229 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.786 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9711 0 15 0 9726
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039873
X-RAY DIFFRACTIONf_angle_d0.61913434
X-RAY DIFFRACTIONf_dihedral_angle_d14.4023658
X-RAY DIFFRACTIONf_chiral_restr0.0421604
X-RAY DIFFRACTIONf_plane_restr0.0031741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.84010.39051310.30331204X-RAY DIFFRACTION93.95
2.8401-2.88240.37381570.28461251X-RAY DIFFRACTION99.22
2.8824-2.92750.30241330.27381302X-RAY DIFFRACTION99.65
2.9275-2.97550.30361180.261274X-RAY DIFFRACTION99.5
2.9755-3.02680.34721230.2681310X-RAY DIFFRACTION99.44
3.0268-3.08180.36831310.27121299X-RAY DIFFRACTION99.51
3.0818-3.14110.31571180.26011313X-RAY DIFFRACTION99.79
3.1411-3.20510.32161640.25281279X-RAY DIFFRACTION99.59
3.2051-3.27480.35161120.26311297X-RAY DIFFRACTION99.65
3.2748-3.3510.35871250.25371293X-RAY DIFFRACTION99.58
3.351-3.43470.33951490.24661294X-RAY DIFFRACTION99.65
3.4347-3.52760.30521520.22951269X-RAY DIFFRACTION99.51
3.5276-3.63130.30891610.21721309X-RAY DIFFRACTION99.53
3.6313-3.74850.28021350.18571243X-RAY DIFFRACTION99.42
3.7485-3.88240.23431450.1821299X-RAY DIFFRACTION99.45
3.8824-4.03770.2431450.17051285X-RAY DIFFRACTION99.1
4.0377-4.22140.23021640.16321292X-RAY DIFFRACTION99.12
4.2214-4.44370.20771420.15771266X-RAY DIFFRACTION98.74
4.4437-4.72190.21871620.14911293X-RAY DIFFRACTION99.59
4.7219-5.0860.25061530.16141273X-RAY DIFFRACTION99.17
5.086-5.59690.271450.17821284X-RAY DIFFRACTION99.17
5.5969-6.40480.28381710.20461279X-RAY DIFFRACTION99.38
6.4048-8.06170.20991440.15741307X-RAY DIFFRACTION98.71
8.0617-44.79140.18591440.14561253X-RAY DIFFRACTION92.27
Refinement TLS params.

Refine-ID: X-RAY DIFFRACTION

IDMethodL11 (°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)
1refined0.74460.56470.94210.4878-0.73391.9340.0330.33220.03240.11210.15530.01180.1671-0.1918-0.00010.7303-0.0577-0.01950.68960.01330.5678-7.5279-30.559668.0396
20.4942-0.22041.18560.48150.77684.74450.0303-0.02350.0837-0.00750.05670.0444-0.18110.1544-00.643-0.0230.04260.46930.00010.6957
31.4985-0.44891.15112.2587-1.03411.23610.1756-0.611-0.2158-0.108-0.20270.0620.0539-0.232-0.68910.54280.04030.07390.96550.13890.4911
41.12350.3637-0.21950.5050.25821.38840.1307-0.9118-0.2748-0.2832-0.15430.04690.32190.13450.00020.68130.02210.09460.89010.3150.7794
50.7606-0.62471.22981.2244-1.84153.96710.0615-0.01670.0890.0164-0.06820.09040.00950.139500.6778-0.06890.02470.73210.04580.7805
61.99470.88340.3170.65110.37121.6539-0.0430.613-0.05250.1367-0.06170.10480.24840.4302-0.03540.62680.0857-0.01390.8184-0.04250.7836
70.25560.0419-0.27270.4207-0.10230.3406-0.3160.3350.439-0.0423-0.08340.1286-0.19060.8974-0.00030.7915-0.00470.14761.11920.05540.8771
80.50690.2945-0.52660.28490.79410.37440.0911-0.4558-0.0203-0.2408-0.1085-0.11840.3666-0.4301-0.00060.85790.0335-0.08930.6656-0.07690.8647
90.04280.05210.12280.0423-0.17670.08190.02881.2671-0.5055-1.07840.1993-0.9448-0.7465-0.22690.00111.2646-0.19080.01640.96590.13550.7913
100.18950.4078-0.14390.3148-0.10960.0321-0.0872-0.13940.8407-0.3022-0.2673-0.19890.3213-0.41620.00110.9584-0.07260.03641.23030.0350.8792
110.08280.02410.00270.0453-0.20.26070.07980.2416-0.35550.00590.02510.0133-0.24640.58960.00020.9095-0.04930.03660.96710.02710.9708
12-0.12580.07720.1419-0.0262-0.18680.09090.2396-0.9778-0.053-0.4297-0.07920.5340.05410.0627-0.00031.3496-0.1109-0.0551.63470.28321.2412
Refinement TLS groupSelection details: chain D and resid 699-721

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