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- PDB-1i7x: BETA-CATENIN/E-CADHERIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1i7x
TitleBETA-CATENIN/E-CADHERIN COMPLEX
Components
  • BETA-CATENIN
  • EPITHELIAL-CADHERIN
KeywordsCELL ADHESION / E-cadherin / beta-catenin / protein-protein complex / extended interface / armadillo repeat
Function / homology
Function and homology information


lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / uterine epithelium development / Beta-catenin phosphorylation cascade / Apoptotic cleavage of cell adhesion proteins ...lung cell differentiation / epicardium-derived cardiac vascular smooth muscle cell differentiation / mesenchyme morphogenesis / RUNX3 regulates WNT signaling / Regulation of CDH11 function / cardiac vascular smooth muscle cell differentiation / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / uterine epithelium development / Beta-catenin phosphorylation cascade / Apoptotic cleavage of cell adhesion proteins / Disassembly of the destruction complex and recruitment of AXIN to the membrane / hair cycle process / TCF dependent signaling in response to WNT / LRR FLII-interacting protein 1 (LRRFIP1) activates type I IFN production / endoderm formation / mesenchyme development / trachea morphogenesis / Formation of the beta-catenin:TCF transactivating complex / positive regulation of epithelial cell differentiation / Deactivation of the beta-catenin transactivating complex / positive regulation of heparan sulfate proteoglycan biosynthetic process / lung induction / positive regulation of branching involved in lung morphogenesis / cranial ganglion development / renal vesicle formation / renal inner medulla development / renal outer medulla development / nephron tubule formation / beta-catenin-ICAT complex / genitalia morphogenesis / embryonic skeletal limb joint morphogenesis / canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation / neural plate development / metanephros morphogenesis / desmosome assembly / glial cell fate determination / regulation of secondary heart field cardioblast proliferation / astrocyte-dopaminergic neuron signaling / animal organ development / oviduct development / beta-catenin-TCF7L2 complex / regulation of nephron tubule epithelial cell differentiation / regulation of timing of anagen / regulation of branching involved in salivary gland morphogenesis / negative regulation of mitotic cell cycle, embryonic / VEGFR2 mediated vascular permeability / regulation of epithelial cell differentiation / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / central nervous system vasculogenesis / salivary gland cavitation / regulation of centriole-centriole cohesion / Degradation of beta-catenin by the destruction complex / Adherens junctions interactions / glandular epithelial cell differentiation / regulation of centromeric sister chromatid cohesion / embryonic axis specification / Ca2+ pathway / RHO GTPases activate IQGAPs / ventricular compact myocardium morphogenesis / morphogenesis of embryonic epithelium / Degradation of the extracellular matrix / Scrib-APC-beta-catenin complex / lens morphogenesis in camera-type eye / beta-catenin-TCF complex / endodermal cell fate commitment / acinar cell differentiation / dorsal root ganglion development / Integrin cell surface interactions / synaptic vesicle clustering / positive regulation of fibroblast growth factor receptor signaling pathway / proximal/distal pattern formation / neuron fate determination / positive regulation of cell-cell adhesion / layer formation in cerebral cortex / positive regulation of myoblast proliferation / establishment of blood-retinal barrier / dorsal/ventral axis specification / lateral loop / sympathetic ganglion development / fungiform papilla formation / desmosome / positive regulation of endothelial cell differentiation / presynaptic active zone cytoplasmic component / mesenchymal to epithelial transition / embryonic foregut morphogenesis / hindbrain development / lung epithelial cell differentiation / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / regulation of protein localization to cell surface / cellular response to indole-3-methanol / mesenchymal stem cell differentiation / smooth muscle cell differentiation / positive regulation of odontoblast differentiation / regulation of osteoclast differentiation / endothelial tube morphogenesis / mesenchymal cell proliferation involved in lung development / midbrain dopaminergic neuron differentiation / regulation of neuron migration
Similarity search - Function
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 / Cadherin / Catenin binding domain superfamily ...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 / Cadherin / Catenin binding domain superfamily / Cadherin conserved site / Cadherin domain signature. / Cadherin repeats. / Cadherin domain / Cadherin-like / Cadherins domain profile. / 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 / Catenin beta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHuber, A.H. / Weis, W.I.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2001
Title: The structure of the beta-catenin/E-cadherin complex and the molecular basis of diverse ligand recognition by beta-catenin.
Authors: Huber, A.H. / Weis, W.I.
#1: Journal: J.BIOL.CHEM. / Year: 2001
Title: The Cadherin Cytoplasmic Domain is Unstructured in the Absence of Beta-Catenin: A Possible Mechanism for Regulating Cadherin Turnover
Authors: Huber, A.H. / Stewart, D.B. / Laurents, D.V. / Nelson, W.J. / Weis, W.I.
#2: Journal: Cell(Cambridge,Mass.) / Year: 2000
Title: Crystal Structure of a Beta-catenin/Tcf Complex
Authors: Graham, T.A. / Weaver, C. / Mao, F. / Kimelman, D. / Xu, W.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Three-dimensional Structure of the Armadillo Repeat Region of Beta-catenin
Authors: Huber, A.H. / Nelson, W.J. / Weis, W.I.
History
DepositionMar 10, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-CATENIN
B: EPITHELIAL-CADHERIN
C: BETA-CATENIN
D: EPITHELIAL-CADHERIN


Theoretical massNumber of molelcules
Total (without water)151,6964
Polymers151,6964
Non-polymers00
Water36020
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)180.8, 134.2, 94.2
Angle α, β, γ (deg.)90.0, 94.3, 90.0
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BETA-CATENIN


Mass: 58844.117 Da / Num. of mol.: 2 / Fragment: ARMADILLO DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: CATNB / Production host: Escherichia coli (E. coli) / References: UniProt: Q02248
#2: Protein EPITHELIAL-CADHERIN / E-CADHERIN


Mass: 17004.023 Da / Num. of mol.: 2 / Fragment: CYTOPLASMIC DOMAIN
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 3.75 Å3/Da / Density % sol: 67.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: POLYETHYLENEIMINE TRIS-HCL ISOPROPANOL, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15-10 mg/mlprotein1drop
20.1 %PEI1reservoirpH8.5
3200 mMTris-HCl1reservoirpH7.5
46 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.033 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 23, 1999
Details: 1) Cylindrical 1m long collimating mirror (Rh-coated Si) before monochromator 2) Toroidal focusing mirror 1.2m long (Rh-coated zerodur) after the monochromator
RadiationMonochromator: Double-Crystal Si 111 crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 46268 / Num. obs: 44525 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Limit h max: 60 / Limit h min: -60 / Limit k max: 44 / Limit k min: -60 / Limit l max: 31 / Limit l min: 0 / Observed criterion F max: 177611.65 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.6
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.368 / % possible all: 98.6
Reflection
*PLUS
Num. measured all: 109516
Reflection shell
*PLUS
% possible obs: 98.6 %

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Armadillo repeat domain of murine beta-catenin, PDB code 2bct.

2bct


Resolution: 3→30 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high rms absF: 10000 / Isotropic thermal model: Grouped isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3449 8.1 %Random
Rwork0.196 ---
all0.2 44525 --
obs0.2 42434 94.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 30.8719 Å2 / ksol: 0.286341 e/Å3
Displacement parametersBiso max: 200.81 Å2 / Biso mean: 59.09 Å2 / Biso min: 2.07 Å2
Baniso -1Baniso -2Baniso -3
1-6.79 Å20 Å2-5.21 Å2
2--0.65 Å20 Å2
3----7.44 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.63 Å0.51 Å
Luzzati d res high-3
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8910 0 0 20 8930
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg18.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.85
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
3-3.140.3153756.60.31845760.0165645495187.7
3.14-3.30.273967.10.27146730.0145558506991.2
3.3-3.510.2654277.60.26447820.0135615520992.8
3.51-3.780.2264658.30.22548680.015583533395.5
3.78-4.160.1794307.70.17750270.0095593545797.6
4.16-4.760.1484357.70.14650430.0075619547897.5
4.76-5.990.1774738.40.17950310.0085620550497.9
5.99-29.710.1484487.80.14949850.0075708543395.2
Xplor fileSerial no: 1 / Param file: protein_rep.param
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 8.1 % / Rfactor all: 0.2 / Rfactor obs: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.2
LS refinement shell
*PLUS
Rfactor Rfree: 0.315 / % reflection Rfree: 6.6 % / Rfactor Rwork: 0.318

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