[English] 日本語
Yorodumi
- PDB-3ifq: Interction of plakoglobin and beta-catenin with desmosomal cadherins -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / CDH11 homotypic and heterotypic interactions / desmosome assembly ...gamma-catenin-TCF7L2 complex / endothelial cell-cell adhesion / 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 / CDH11 homotypic and heterotypic interactions / desmosome assembly / Regulation of CDH19 Expression and Function / regulation of branching involved in salivary gland morphogenesis / salivary gland cavitation / Adherens junctions interactions / Regulation of CDH11 function / RHO GTPases activate IQGAPs / Degradation of the extracellular matrix / Integrin cell surface interactions / positive regulation of cell-cell adhesion / zonula adherens / lateral loop / desmosome / regulation of protein localization to cell surface / cellular response to indole-3-methanol / detection of mechanical stimulus / regulation of neuron migration / epithelial cell morphogenesis / alpha-catenin binding / trophectodermal cell differentiation / Formation of the cornified envelope / bicellular tight junction assembly / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / Schmidt-Lanterman incisure / cornified envelope / flotillin complex / intestinal epithelial cell development / cell-cell adhesion mediated by cadherin / catenin complex / regulation of ventricular cardiac muscle cell action potential / node of Ranvier / Adherens junctions interactions / negative regulation of protein processing / intermediate filament / positive regulation of cell-matrix adhesion / apical junction complex / RHOB GTPase cycle / skin development / cochlea development / RHOC GTPase cycle / RHOJ GTPase cycle / homophilic cell adhesion via plasma membrane adhesion molecules / RHOQ GTPase cycle / regulation of heart rate by cardiac conduction / microvillus / negative regulation of blood vessel endothelial cell migration / CDC42 GTPase cycle / RHOH GTPase cycle / decidualization / intercalated disc / RHOA GTPase cycle / establishment of skin barrier / canonical Wnt signaling pathway / negative regulation of protein localization to plasma membrane / cytoskeletal protein binding / cell adhesion molecule binding / positive regulation of protein localization / axon terminus / embryo implantation / positive regulation of DNA-binding transcription factor activity / protein localization to plasma membrane / VEGFR2 mediated vascular permeability / nuclear receptor binding / cell periphery / adherens junction / cellular response to amino acid stimulus / sensory perception of sound / negative regulation of canonical Wnt signaling pathway / protein-DNA complex / beta-catenin binding / cell-cell adhesion / Z disc / cytoplasmic side of plasma membrane / positive regulation of protein import into nucleus / specific granule lumen / positive regulation of angiogenesis / negative regulation of epithelial cell proliferation / positive regulation of canonical Wnt signaling pathway / apical part of cell / cell-cell junction / cell migration / regulation of protein localization / regulation of cell population proliferation / actin cytoskeleton organization / regulation of gene expression / protein phosphatase binding / basolateral plasma membrane / molecular adaptor activity / in utero embryonic development / ficolin-1-rich granule lumen / cytoskeleton
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 / 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
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more