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- PDB-1i7w: BETA-CATENIN/PHOSPHORYLATED E-CADHERIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1i7w
TitleBETA-CATENIN/PHOSPHORYLATED E-CADHERIN COMPLEX
Components
  • BETA-CATENIN
  • EPITHELIAL-CADHERIN
KeywordsCELL ADHESION / E-cadherin / beta-catenin / protein-protein complex / extended interface / armadillo repeat / phosphoserine
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 / negative regulation of mitotic cell cycle, embryonic / VEGFR2 mediated vascular permeability / negative regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / regulation of branching involved in salivary gland morphogenesis / central nervous system vasculogenesis / regulation of epithelial cell differentiation / salivary gland cavitation / regulation of centriole-centriole cohesion / Degradation of beta-catenin by the destruction complex / Adherens junctions interactions / regulation of centromeric sister chromatid cohesion / embryonic axis specification / Ca2+ pathway / RHO GTPases activate IQGAPs / 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 / endothelial tube morphogenesis / ventricular compact myocardium morphogenesis / layer formation in cerebral cortex / dorsal/ventral axis specification / lateral loop / sympathetic ganglion development / establishment of blood-retinal barrier / positive regulation of myoblast proliferation / fungiform papilla formation / desmosome / positive regulation of endothelial cell differentiation / presynaptic active zone cytoplasmic component / mesenchymal to epithelial transition / hindbrain development / lung epithelial cell differentiation / positive regulation of determination of dorsal identity / positive regulation of skeletal muscle tissue development / ectoderm development / fascia adherens / regulation of protein localization to cell surface / embryonic foregut morphogenesis / cellular response to indole-3-methanol / smooth muscle cell differentiation / positive regulation of odontoblast differentiation / regulation of osteoclast differentiation / mesenchymal cell proliferation involved in lung development / histone methyltransferase binding / mesenchymal cell proliferation / alpha-catenin binding
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: 2 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 9, 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 ...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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,59114
Polymers152,1764
Non-polymers41410
Water12,052669
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13150 Å2
ΔGint-222 kcal/mol
Surface area44850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.6, 85.3, 115.1
Angle α, β, γ (deg.)90.0, 107.9, 90.0
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-957-

HOH

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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: 17243.965 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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 669 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: polyethylene glycol monomethylether 5000, Tris-HCl, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15-10 mg/mlprotein1drop
213.5 %(w/v)PEG50001reservoir
3200 mMTris-HCl1reservoirpH8.0
41.1 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 26, 2000
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: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. all: 107020 / Num. obs: 101570 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 24.3 Å2 / Limit h max: 78 / Limit h min: -84 / Limit k max: 42 / Limit k min: -84 / Limit l max: 57 / Limit l min: 0 / Observed criterion F max: 408469.96 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.339 / % possible all: 94.9
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 287321 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 94.9 %

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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: 2→100 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 0.3 / Data cutoff high rms absF: 10000 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.245 5330 5.5 %Random
Rwork0.206 ---
all0.208 101570 --
obs0.208 96075 91.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 59.3926 Å2 / ksol: 0.367974 e/Å3
Displacement parametersBiso max: 117.29 Å2 / Biso mean: 47.05 Å2 / Biso min: 14.13 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å2-11.69 Å2
2---0.38 Å20 Å2
3---1.52 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.3 Å
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 2→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8685 0 10 669 9364
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg18.5
X-RAY DIFFRACTIONx_torsion_impr_deg0.86
X-RAY DIFFRACTIONx_mcbond_it2.031.5
X-RAY DIFFRACTIONx_mcangle_it2.792
X-RAY DIFFRACTIONx_scbond_it3.152
X-RAY DIFFRACTIONx_scangle_it4.322.5
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 (%)
2-2.090.3294343.30.328102050.016130901063981.3
2.09-2.20.2785394.10.277107350.012130601127486.3
2.2-2.340.2426334.80.241111210.01130691175489.9
2.34-2.520.2265784.40.227114690.009131221204791.8
2.52-2.770.2216675.10.222115990.009130831226693.8
2.77-3.170.2257165.50.225119110.008131321262796.2
3.17-40.1838986.80.182118610.006131721275996.9
4-76.980.1758656.50.176118440.006133541270995.2
Xplor fileSerial no: 1 / Param file: protein_rep.param
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å / σ(F): 0 / % reflection Rfree: 5.5 % / Rfactor obs: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / % reflection Rfree: 3.3 % / Rfactor Rwork: 0.328

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